28-year-old Sister Abhaya murder case: The longest running investigation

The CBI unit of Thiruvananthapuram had recently found a significant lead in a 28-year-old case related to the murder of a Catholic nun in Kottayam. The two accused – Priest Thomas Kottoor and Nun Sister Sephy were found guilty of murder in one of the longest running cases.

Kottoor (71-year-old), a scholar in Moral Theology, is the first accused, and Sephy (57-year-old) is the second accused in the case.

On March 27th, 1992, the State Police had initially concluded that the 21-year-old nun, Sister Abhaya, a student of Kottayam’s BCM College, and a member of the Knanaya Catholic Community committed suicide.

After the protest led by activist Jomon Puthenpurackal had started with a campaign to seek justice for the nun, the case was handed over to CBI.

The Incident:

Sister Abhaya was found dead in a well in St Pius X Convent in Kottayam on 27th March 1992.

Local Police and the Crime Branch of the State Police had at the time said it was a case of suicide.

However, a year later, the Central Bureau of Investigation (CBI) took over the case when Sister Banicassia, Mother Superio, and 67 other nuns from the Knanaya Catholic Church wrote to the Chief Minister K. Karunakaran, claiming the probe wasn’t conducted properly. At the same time, activist Jomon Puthenpurackal took the matter to court on the same grounds.

Father Thomas Kottoor, Sister Sephy, and Sister Abhaya were all part of the Knanaya Catholic Church, headquartered in Kottayam. Sister Abhaya, who was in her early 20s, was a student in the graduation College run by the church where Father Kottoor, who was also secretary to the Bishop, taught psychology.

She lived in Pious Xth Convent Hostel, the place of crime. Sister Sephy stayed in the same hostel and was its de facto in-charge.

Series of Events:

Sister Abhaya was reported missing on the morning of 27 March 1992.

She had woken at 4:00 am to study for exams and was last known to have gone to the kitchen for a drink.

The refrigerator door was left ajar, a bottle of water was spilled on the floor and a single slipper sat under the fridge – its pair was found beside the convent hostel’s well.

After a brief search, Sister Abhaya’s body was found in the convent hostel’s well in the early hours of the same day. Kottayam West Police Station upgraded their investigation to that of unnatural death.

At 10:00 am, the deceased was removed from the well by the fire force and an inquest was drawn up.

A post-mortem conducted on the body by Dr. Radhakrishnan of Kottayam Medical College found abrasions on the right shoulder and hip and two small lacerations above the right ear.

There was no sign of sexual assault. Despite the potentially significant injuries, the death was concluded to happen through drowning.

The series of inquiries by various investigating bodies that followed was lengthy, convoluted, and unsatisfactory, plagued by internal conflict, bitter rivalries, and allegations of corruption and bias, compounded by pressure from many quarters to bring the case to conclusion.

In April 1992, the Crime Branch of the Criminal Investigation Department took up the case, and months later ruled Sister Abhaya’s death a suicide. However, the Crime Branch was alleged to have destroyed crucial material evidence potentially implicating homicide as a cause of death.

In April 1995, forensic medical experts Dr. S K Pathak, Dr. Mahesh Verma, and Dr. S R Singh conducted dummy experiments leading them to conclude that homicide could not be ruled out.

Nevertheless, no arrests were made until November 2008. After years of failed investigations and internal struggles, two priests – Thomas Kottoor, Jose Puthurukkayil, and a nun – Sister Sephy – were arrested by the Crime Branch on 19 November 2008.

All three suspects were granted bail in early January 2009.

On 17 July 2009, the three were charged with murder, defamation, and destruction of evidence.

Prosecutors alleged that Sister Abhaya had stumbled upon the two priests and one sister in a “compromising position” and had subsequently been attacked with an axe and dumped in the well.


a) Action Council

An Action Council was convened by Jomon Puthenpurackal in 1992 demanding prosecution of those responsible for the murder of Abhaya.

67 nuns belonging to Abhaya’s congregation petitioned to the Chief Minister of the Kerala State Government to investigate the case as a homicide.

On 7 April 1992, the Director-General of Police of Kerala directed the Crime Branch of the Kerala Police to take over the investigation from the local police. The Kerala Government, based on the petition, recommended a CBI enquiry. On 29 March 1993, CBI began a new investigation.

b) Kerala Police

On 27 March 1992, Kottayam West Police Station ASI V V Augustine visited the crime scene and called the fire force to search for Abhaya’s body in the well in the compound. The fire force removed the body from the well. An inquest was prepared by ASI Augustine. Later, the ASI was said to kill himself in 2008. Photographs of the body were also taken. Clothing of Abhaya was taken into custody. Later these items of physical evidence were destroyed. The post-mortem report indicated death by drowning but also reported on the possibility of homicide based on head injuries.

On 7 April 1992, the Director-General of Police of Kerala directed the Crime Branch section of the Kerala police to take up the investigation. The Crime Branch submitted its report before the Revenue Divisional Officer (RDO) on 30 January 1993. The Crime Branch concluded that Abhaya had committed suicide. According to the postmortem report, she had died from drowning. Though there were allegations that the Crime Branch had procured the evidence in the case from the court and destroyed it, this was subsequently disproved by the CBI.

c) CBI

On 29 March 1993, the FIR in the case was registered by the CBI. The CBI started investigating the death of Sister Abhaya under the direct supervision of its officer Varghese P. Thomas.

On 29 November 1996, the CBI issued the first final report. The author of the report, A.K. Ohri, stated that he could not determine whether Abhaya’s death was suicide or homicide. The report was not accepted by the Chief Judicial Magistrate’s Court.

On 9 July 1999, the CBI issued a second final report authored by Surinder Paul. Paul concluded that Abahya’s death was a homicide, but he could not establish the identity of the perpetrators. Paul’s report was also not accepted by the court.

On 25 August 2005, the CBI issued yet another report, authored by R.R. Sahay. Sahay concluded that there was no indication that anyone was involved in Abhaya’s death. The report was again not accepted.

On 4 September 2008, the court turned the investigation over to the Cochin branch of the CBI.

Some of the initial manipulations in the case by the local police and crime branch, alleged by CBI are:

-The investigation report did not indicate the homicidal injuries on the body of Abhaya.

-The material evidence in the case was destroyed and the clothes were not subject to forensic examination.

-The photographs showing injuries on the body were removed.

-The crime scene was tampered with or material physical evidence was not collected from the crime scene.

During the initial inquiry, the post-mortem, chemical examination, and laboratory report also had been erased and then rewritten due to other influences.

On 30 December 1993, Varghese P. Thomas resigned from the service of CBI and the investigation of Abhaya’s death. He had seven more years in service to retire. He had concluded that Abhaya’s death was a case of murder and he had recorded it as such in the Case Diary.

Subsequently, on 19 January 1994, he called a special press conference in Cochin and announced that he had resigned from CBI as his conscience did not permit him to comply with a strong directive given by his superior officer, V. Thyagarajan, the then Superintendent of CBI Cochin Unit, who had asked Varghese P. Thomas to record the death of Abhaya as suicide in the Case Diary. With this press conference, the case of Abhaya caught media attention all over India and the matter was strongly debated in the parliament as well as in the Kerala state assembly on several occasions.

d) Writ Petition to Kerala High Court

The Action Council filed another writ petition in the Kerala High Court asking the court to remove V. Thyagarajan from the Kerala Unit of the CBI as well as from the investigation. Further on 3 June 1994, all the MPs from the state jointly submitted a passionate petition to K. Vijaya Rama Rao, the Director of the CBI requesting him to disallow Thyagarajan to continue in the Abhaya’s murder case. As a result, M.L. Sharma, the Joint Director of the CBI, was given charge of the investigation into Abhaya’s death.

Timeline of the Case:

Three years after taking over the case by CBI, in the year 1996, the CBI said it couldn’t yet conclude if this was a suicide or homicide.

The Chief Judicial Magistrate Court rejected the report and directed CBI to continue with the investigation.

In March 1997, CBI submitted its second report in which it stated that the death was a homicide, based on the medical opinion of three doctors. Despite efforts though, however, the identity of the accused could not be established.

By August 2005, when the CBI submitted its final report, it had not yet managed to unveil the identity of the culprits.

“….further investigation conducted, at the behest of the court, has not indicated involvement of any person in the death of Sister Abhaya,” the report stated with a request to close the case as ‘untraced’ for the case to be treated “as closed being untraced.”

In the year 2008, the Kerala High Court handed the case to the CBI’s Kerala Unit, giving it three months to investigate.

The new investigation was led by Deputy Superintendent of Police Nandakumar Nair. His team recorded a statement from Sanju P. Mathew, who lived next to the hostel.

Mathew in his statement stated that he had seen Father Kottoor on the campus on the day of the crime. This finally led to the arrest of Father Kottoor, Sister Sephy, and Father Jose Puthurukkayil in November 2008. All the three accused were granted bail by the Kerala High Court six months later.

CBI filed the charge sheet against the accused in July 2009.

In 2018, Father Jose Puthurukkayil was acquitted due to a lack of evidence.

Allegations of Evidence Tampering:

In July 2007, the CBI received the court’s approval to undergo narco-tests on the suspects of the case. As such, the tests were conducted on August 3, 2007, in Bengaluru. Following the tests, the CBI informed the Court that the investigative team found ‘no new facts’ in the case.

However, it was soon unearthed that the master tapes of the test results were tampered with. The revelation came after the technical experts at the Center for Development of Imaging Technology (C-DIT) in Thiruvananthapuram had investigated the tapes as a part of a forensic probe – directed by CIM court in Kochi. It was found that the tape was edited at 30, 23, and 19 places respectively.

In December 2019, the Kerala High Court ruled that the brain mapping and narco-analysis cannot be used as evidence, even if the consent of the accused is sought.

The Court said that the test results can only be used to prove ‘discovery of fact’ as per the Indian Evidence Act (section 27)

CBI’s findings:

As per CBI’s findings, Sister Sephy was having an “affair” with the two other accused and had been caught by Abhaya on the day of the crime.

Abhaya had apparently seen the three in a compromising position when she had gone to the kitchen to get water from the refrigerator around 4 am. To silence her, Father Kottoor is believed to have strangled Abhaya while Sister Sephy hit her with an axe. The accused then dumped her body in the well.

Adakka Raju, a thief who had broken into the convent that morning, said he saw both priests there. Raju was a key witness in the case, which saw eight of the forty-nine witnesses turn hostile during the trial.

The CBI case included circumstantial evidence such as a water bottle, a veil, an axe, a basket, and Sister Abhaya’s slippers, besides narco-analysis and brain mapping of the accused.

Circumstantial Evidence relied upon by CBI:

The most crucial evidence relied upon by the CBI had been the disturbance in the kitchen

The water bottle had fallen near the fridge with dripping water, the veil was found underneath the exit door, which was found locked from the outside- the latches inside were unlatched.

An axe and a basket had fallen, pair of slippers of Abhaya were found at different places in the kitchen, and altogether, the area exhibited an appearance of having had a tussle inside. But there was no blood at the scene.

Recent findings:

The priest and nun are found guilty of murder and are sentenced to life imprisonment.

The Priest – Father Kottoor was charged under sections 302, 201, and 449 of the Indian Penal Code (IPC), whereas Sister Sephy was booked under sections 201 and 302 of the IPC.

*Link of the source

*Link of the source

Research by Khushboo Asrani

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