The court sought a response from the jail authorities by June 8 on the convict's plea.
Bhatkal alleged physical harassment in the prison, while urging the court to direct a probe by the CBI and the Anti Corruption Branch in this regard.
In his plea, moved through his lawyer M S Khan, the convict alleged that he had been kept in isolation for the last four months, due to which he was suffering from mental and psychological problems.
Bhatkal was sentenced to death by an NIA court in December last year in the 2013 Dilsukhnagar twin blasts case in Hyderabad. He is at present in judicial custody in connection with several other terror-related cases.