Defence counsel Jethmalani said the Shankaracharya was denied his fundamental right under Articles 21 and 22 of the Constitution.
The detention comes a day after the charge sheet was filed against Kanchi Shankaracharya Jayendra Saraswati and the junior seer in the case.
The police questioned two Kanchi Mutt officials in connection with the assault on former Mutt official Radhakrishnan
The Uttaradhi Mutt's 40-year-old manager was found dead on Thursday morning.
The Tamil Nadu chief minister dismissed apprehensions that the arrest would disrupt daily prayers at the mutt.
The seer 'is not in any angry or uncooperative mood', but is mostly replying in the negative. He slept most of the time since he seemed to be exhausted, the police said.
The Kanchi seer should resign to protect the respect and dignity of the post occupied by him, he said.
Some 18 people have been held in the murder of Sankararaman, manager of the Varadaraja Perumal temple on Sept 3.
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The Kanchi seer has moved the Principal Sessions Court in Chennai for anticipatory bail, apprehending arrest in another case.
The seer is charged with having a role in the murder of a Kanchipuram temple official A Sankararaman.
The day-long bandh has been called by the VHP to give vent to the feelings of Hindus over the unjust arrest of the Kanchi seer.
Based on information provided by two people arrested in Chennai on November 9, the police got information about the seer's links with those hired to murder the temple official, she said.
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The court directed the Tamil Nadu police to produce the entire case diary in original before it on January 6 for further hearing.
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Veteran journalist Cho Ramaswamy says the Tamil Nadu police wouldn't have acted without solid evidence against the seer.
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Kanchi Mutt head Jeyendra Saraswati on Thursday said the Mutt is fully prepared to take on the restoration of the Shiva temple of Kedarnath that has been ravaged by the recent floods. "The Mutt has made arrangements to assess the nature and damage to the temple, if any. The temple, which is a monument of our country's heritage and cultural richness, should not be tampered with. The fact that it withstood the natural calamity all around itself is proof of sanctity," he said.
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A local court on Thursday adjourned to April 4 hearing in the Sankararaman murder case in which Kanchi seer Jayendra Saraswati and his junior Vijayendra are the prime accused.
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A local court on Wednesday adjourned to August 1 hearing in the Sankararaman murder case in which Kanchi seer Jayendra Saraswathi and his junior Vijayendra, are the prime accused.