Raghu has been charged with murder and conspiracy.
The SC verdict granting bail to the seer due to 'lack of evidence is beyond the tolerance of the prosecution and its sole aim is to tarnish the reputation of the mutt', Murli Manohar Joshi said.
Vijayendra Saraswathi, 48, had become the 70th acharya of the Kanchi Kamakoti Peetam on May 29, 1983.
Sundaresa Iyer is a confidant of incarcerated Kanchi Shankaracharya Jayendra Saraswati, who is the prime accused in the murder of temple official Sankararaman and the assault on former mutt employee Radhakrishnan.
The burial ceremony was performed in the presence of Sri Vijayendra Saraswathi, the junior pontiff of the Mutt and some close family relatives of the late seer.
The Supreme Court on Monday granted him bail in the Sankararaman murder case with the condition that he will not visit the Kanchi mutt till investigations in the case are over.
The police questioned two Kanchi Mutt officials in connection with the assault on former Mutt official Radhakrishnan
The arrest was made at the Kanchi mutt at around 1800 IST.
'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 seer is accused of masterminding the assault on a former auditor of the mutt.
Since a chargesheet has been filed in the Sankararaman murder case, the bail conditions prohibiting his entry into the mutt no longer apply, police said.
. Jayendra also offered 'arthi' to the idol of Adi Sankara, Mutt sources said.
The detention comes a day after the charge sheet was filed against Kanchi Shankaracharya Jayendra Saraswati and the junior seer in the case.
There is evidence that Sankararaman had more resentment towards the junior seer, his brother Raghu and Sundaresa Iyer than the senior seer, the judge said.
They have been booked under Section 20(1) of the Narcotics Drugs and Psychotropic Substances Act for "contravention in relation to canabis plant and canabis."
Kanchi Shankaracharya Jayendra Saraswati on Thursday filed another petition in the Supreme Court seeking bail in a attempt-to-murder case.
Key accused Appu alias Krishnasamy and Kathiravan were brought from Cuddalore and Tiruchirapalli prisons respectively and produced before the court.
This one relates to an attack on a former official of the Kanchi Mutt, G Radhakrishnan, and two others in September 2002.
Kanchi Sankaracharya Jayendra Saraswathi and eight others were on Friday acquitted of all charges, including attempt to murder, in the 2002 the auditor Radhakrishnan assault case.
So, he approached Rajiv Gandhi and the then president Venkataraman and was advised by both to accept it only if no other job was available.
Jayendra Saraswati returned to the Kacnhi Mutt for the first time this year.
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.
The junior seer has now be questioned twice in three days.
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 HC rejected the seers' bail application on Wednesday.
The Kanchi seer should resign to protect the respect and dignity of the post occupied by him, he said.
The seer is charged with having a role in the murder of a Kanchipuram temple official A Sankararaman.
Veteran journalist Cho Ramaswamy says the Tamil Nadu police wouldn't have acted without solid evidence against the seer.
After hearing arguments of both the defence and prosecution, the magistrate at the Sessions Court, Chengalpattu, Akbar Ali, reserved the orders for January 27.
In his application, Vijayendra said he apprehended arrest following the alleged confessional statements made by Appu and Ravi Subramaniam, both accused in the case.
Earlier in the day, the magistrate had extended the judicial remand of Ravi Subramaniam, who had turned approver in the case, till February 3.
The Judge directed Public Prosecutor Duraisamy to inform the court the government's stand by 1500 IST on Friday and file his counter.
In a huge relief to the pontiffs of Kanchi Sankara Mutt, Jayendra Saraswathi and Vijayendra Saraswathi, a local court on Wednesday acquitted them in the murder case of a temple official in Kancheepuram in Tamil Nadu.
"The swamiji is of the view that only a CBI probe can help get to the truth and ensure justice."
Mutt advocate A Shanmugham told the \nthe Special Investigation Team probing the cases against the Kanchi seers that the summons were not legally enforceable.