Kanchi Shankaracharya Jayendra Saraswathi was Tuesday charged with a second murder and police claimed to have enough evidence for filing a third criminal case against him.
The developments came even as a family demanded a probe into the death of two students of the mutt.
According to the police, the new criminal cases were based on confessions of the 18 people in custody in connection with the murder of Sankara Raman, a former accountant of the mutt, in Kanchipuram Sep 3 that led to the arrest of the pontiff Nov 11.
Police said some of the people in custody in the case confessed to their involvement in a murderous assault on Radhakrishnan, a detractor of the pontiff, and his family in September 2002 in Chennai.
The police are also investigating an assault allegedly at the behest of the pontiff on another dissident, Madhavan.
The demand for fresh probe has come from a family in Kerala that told the media it suspected foul play in the death of Kesavan Namboothiri, who was studying in the mutt's vedic institute, in 1985.
The mutt has said the Kesavan Namboothiri died of electrocution in "an accident".
The body of his close friend and classmate Sankaran Namboothiri was found a few weeks later on a railway track near Thrissur in Kerala.
"I now suspect that my brother died of some foul play at Kanchipuram. I cannot simply believe that he died of an electric shock, as the Mutt officials said," Narayanan Namboothiri, Kesavan's brother, told reporters.
He said he had sent a fax message to Tamil Nadu Chief Minister J. Jayalalitha urging an investigation into the two deaths.
Jayendra Saraswathi was sent to Vellore central prison in judicial custody after his three-day police remand ended Monday. His judicial custody ends Nov 26.