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.
Justice A K Rajan reserved his orders on Saturday on the petition filed by the seer.
The BJP has dubbed the seer's arrest as an "assault on religion".
The order on the prosecution application, seeking five days' custody, was delayed for some time.
The Shankaracharya was brought in a convoy of cars from the Vellore prison at 1115 IST to the court of a first class judicial magistrate.
The hearing remained inconclusive today.
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.
Joshi termed as 'absurd notion' the prosecution's view that the Shankaracharya could poison himself if he was allowed to cook his own food in jail.
'The Supreme Court has set certain guidelines on whom to arrest or whom not to arrest for what offence,' he said.
Dharnas, rallies and fast are the means through which the protest is being expressed.
The Judge directed Public Prosecutor Duraisamy to inform the court the government's stand by 1500 IST on Friday and file his counter.
Kanchi Shankaracharya Jayendra Saraswati was arrested near Hyderabad last night as a prime accused in a murder case.
If you had to defuse the ticking time bomb, how would you do it?
Kanchi Shankaracharya Jayendra Saraswathi offered the crown costing Rs 1.5 crore.
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.
According to Yadav's counsel, the two cases have a lot in common.
Granting the bail, Justice R Balasubramaniam directed the Seer to furnish a personal bond for Rs 25,000 with two sureties for like amount.
The court directed the Tamil Nadu police to produce the entire case diary in original before it on January 6 for further hearing.
"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.
'The Shankaracharya's supporters are shooting the messenger. What is Jayalalithaa's fault? Is it that she has allowed law to take its own course? Is she not supposed to?' asks Tamil Nadu government counsel, K T S Tulsi.
The Madras high court rejected Jayendra Saraswathi's petition challenging a Kanchipuram court order to send him to police custody.
The outfit also refused to comment on the rejection by the Muslim Law Board of Kanchi seer's proposals to resolve the Ayodhya issue.
The 10-day long event, called Mahamaham, will take place in Kumbakonam in Tamil Nadu.
VHP leader Pravin Togadia insisted any negotiated settlement should involve handing over the disputed site to Hindus unconditionally.
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'.
On Sunday, he had said that Muslim religious leaders were prepared to hand over the disputed site in Ayodhya to Hindu religious heads.
Part II of the Kanchi Shankaracharya's exclusive interview to rediff.com
He urged Muslims not to make Ayodhya a 'prestige issue'.
The outfit's international president Ashok Singhal said there was no need for a new mosque in Ayodhya.
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