A CBI spokesman said Father Thomas Kottor, Father Joes Phthrukayil and Sister Abey were arrested by the agency's Special Crime unit.
This is the first arrest in the case that shocked Kerala after the 21-year-old sister was found dead in a well in St Pius convent in Kottayam on 27 March, 1992.
Sister Abhaya, daughter of M Thomas hailing from Areekara, was a second year pre-degree student in BCM college at Kottayam in 1992. The college belonged to the diocese of Kottayyam.
The local police who first investigated the matter could not bring out any evidence to prove the murder. The case was transferred to the Kerala Crime Branch on April 7, 1992 which claimed that Abhaya had committed suicide.
In the meantime, the Action Council, constituted for justice for Sister Abhaya, approached the Kerala High Court which directed the CBI to investigate the matter on March 29, 1993.
The CBI had earlier filed three closure reports which were rejected by the High Court.
According to unconfirmed reports, the CBI has also arrested Sister Sephy, a nun in connection with the case.
The CBI had earlier conducted narco analysis and polygraph tests on the two priests and Sister Sephy.
On September 4, 2008, the Kerala High Court directed the CBI Delhi unit, which was investigating the case, to hand over the probe to its Kochi unit after observing that an ‘unseen hand’ was at work to ‘jettison’ the truth in the sensational case.
Sister Abhaya's body was found in the well of the St Pius convent on March 27, 1992. The local police and crime branch investigated the case and had concluded that it was a case of suicide.
The CBI took over the case on March 29, 2003, and filed three closure reports, saying though it was a case of murder, the suspects could not be found. The High Court refused to accept the report and asked the probe agency to further investigate.