Sri Jayendra Saraswathi was arrested in November
Institutions in the Indian state of Tamil Nadu run by the religious establishment, the Kanchi Shankara Mutt, are facing a financial crisis.
Several cheques issued by the establishment, which is headed by Hindu seer, Sri Jayendra Saraswathi, have been rejected by the banks.
The seer is facing murder charges and was recently freed on bail.
Police have frozen the monastery's bank accounts because of problems over legal documents handed to them.
They say the seer's legal team gave them incorrect documentation relating to the establishment's bank accounts.
'Afraid'
A lawyer for Sri Jayendra Saraswathi's Kanchi Shankara Mutt has said that police have frozen 183 bank accounts held by the monastery and its trusts.
But there has been no official confirmation or denial of that from the authorities in Tamil Nadu.
Some officials at the monastery say their problems have further increased as devotees are now afraid to offer open support after police questioned frequent visitors to the monastery - including the devotees and some journalists.
Sri Jayendra Saraswathi was freed on bail on Tuesday after spending two months in prison.
But he has been barred from returning to the Kanchi monastery.
His deputy, Sri Vijayendra Saraswathi, who became interim leader when the senior seer was arrested in November, was arrested on Monday in connection with the investigations.
Meanwhile, reports say India's National Human Rights Commission has sought an explanation from the Tamil Nadu police on the junior pontiff's arrest and leaking of select video clips to the media which showed the police questioning of Sri Jayendra Saraswathi.
The clips were aired by some private television channels on Friday.
The TV channels said they had received the tapes from unidentified people and that police did not object to their broadcast.
The clips showed the senior seer telling his interrogators that his deputy did not care for him and was instead worried about the possibility of police detaining him and his brother.
The seer was also shown saying that he was troubled by the critical letters written by former aide, Sankararaman, who was later murdered.
Police have, however, denied that they had anything to do with the broadcast of the video clips.