Police have detained Raghu, the younger brother of junior Sankaracharya Vijayendra Saraswati, under a tough law.
Police are investigating the murder of temple official Sankararaman.
Under the Goondas' Act, it would be difficult for Raghu to come out of jail on bail.
The Sankara Mutt manager Sundaresa Iyer was also arrested under the Goondas' Act.
The two are lodged in the Central Prison here after being charged as the third and fourth accused in the murder case, in which two Sankaracharyas, Jayendra Saraswati and Vijayendra Saraswati, were arraigned as the prime accused.
Eight others charged in the murder case, including the leader of the killer gang Kathiravan and his seven associates, were already detained under the Goondas' Act.
The investigators clarified yesterday that the real estate dealer Ravi Subramaniam, originally cited as accused number two, was not included among the list of 24 charged in the murder as he had turned approver.
He has been listed as the first witness for prosecution and is no longer an accused, police said.
Meanwhile, the Sankara Mutt lawyer A. Shanmugham said he would move the Supreme Court tomorrow seeking relaxation in the conditions laid down by the Supreme Court while granting bail to the senior Shankaracharya on January 10.
One of the conditions was that the Shankaracharya should not visit the Kanchi Mutt till the filing of the charge sheet.
Now that the charge sheet has been filed on Friday, the Shankaracharya is free to return to his headquarters but he is yet to make up his mind.
Commenting about the charge sheet, Shanmugham said he was confident that the Mutt and the two Shankaracharya would emerge unscathed since the prosecution seemed to rely heavily on the statement made by the accused-turned-approver Ravi Subramaniam.
"They have filed so many files and records but are relying on Ravi's confessional statement, which will in no way affect our case," the Mutt lawyer said.
The state opposition leader, M Karunanidhi, has come up with his own sarcastic interpretation of the charge sheet.
The Mutt devotees should indeed laud the devotion shown by the investigating team in first worshipping at the Varadaraja Perumal Temple and also choosing auspicious time before filing the charge sheet in the court.
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