Sankararaman's widow has opposed the petition seeking transfer of the case outside Tamil Nadu.
The order on the prosecution application, seeking five days' custody, was delayed for some time.
He told Paul Dinakaran that some people were misleading the minority community on the issue to gain political mileage.
The prosecution had told the Madras high court on Monday that the pontiff had extensive telephonic conversations with Usha at Srirangam.
The Judicial Magistrate-I court in Kanchipuram had issued summons to the seer asking him to appear before the court to receive the copy.
"It (mosque) should be built where it is required....It is not required in Ayodhya where people are already worshipping...," the seer told NDTV 24X7.
The pontiff's fresh peace initiative has been rejected by both the Vishwa Hindu Parishad and the All India Muslim Personal Law Board while the Centre has termed it as a 'personal initiative'.
"None is above law. Whatever the misfortune I am suffering, I am okay," the seer was quoted as saying by former Madhya Pradesh chief minister Uma Bharti, who met him in jail in Vellore on Tuesday.
'We don't want him to get embroiled in any controversy,' Minister of State for Home Swami Chinmayananda said.
The junior seer has now be questioned twice in three days.
Some 18 people have been held in the murder of Sankararaman, manager of the Varadaraja Perumal temple on Sept 3.
The court directed the Tamil Nadu police to produce the entire case diary in original before it on January 6 for further hearing.
The NHRC noted that media reports had pointed that Vijayendra Saraswati was arrested within hours of the Supreme Court directing the release of the senior Shankaracharya on bail.
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 Mutt was energised by Pudu Periyava.' 'Instead of people coming to the Mutt, he has taken the Mutt to the people in several dimensions.'
The way things have gone and the way the Shankaracharya has been treated, the people and the nation are concerned."
The Madras high court on Thursday had ordered his release on bail in the Sankararaman murder case.
'It is not possible that the Shankaracharya was arrested in Mehboobnagar without the chief minister of the state consulting the Centre on the issue,' M M Joshi said.
"Though I was not physically tortured, I was mentally and psychologically tortured in police custody. The police officials induced me to speak over mobile to several persons, which I declined with folded hands," he was quoted as saying by NDA MPs.
"Though I was not physically tortured, I was mentally and psychologically tortured in police custody. The police officials induced me to speak over mobile to several persons, which I declined with folded hands," he was quoted as saying by NDA MPs.
Three special teams are on the lookout for the two prime accused, Appu and Ravi Subramaniam.
'The Supreme Court has set certain guidelines on whom to arrest or whom not to arrest for what offence,' he said.
The detention comes a day after the charge sheet was filed against Kanchi Shankaracharya Jayendra Saraswati and the junior seer in the case.
The Tamil Nadu chief minister dismissed apprehensions that the arrest would disrupt daily prayers at the mutt.
"We told the prime minister that it is the question of sentiments of crores of Hindus, hurt by investigations being conducted with a vindictive attitude and the ill-treatment meted out to Jayendra Saraswati," BJP president L K Advani said.
The Supreme Court will give its verdict on the bail application of Kanchi Shankaracharya Jayendra Saraswati in the Sankararaman murder case on Monday.
Tell us what you think about the Kanchi Shankaracharya's arrest.
The seer is charged with having a role in the murder of a Kanchipuram temple official A Sankararaman.
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