Acting Chief Judicial Magistrate Jyotsna Roy ordered Subrata be sent to judicial custody till June three.
Subrata sought permission to submit a declaration under section 164 IPC (recording of confession and statement), but was opposed by Assistant Public Prosecutor Kuntal Chatterjee.
"His appeal was not made following the procedure," Chatterjee said.
Hriday Ghosh, the son of Sagar Ghosh had alleged that his father in his dying declaration had mentioned the name of Subrata Roy and Bhagirath Ghosh.
Sagar Ghosh had won in the panchayat polls as an independent after the Trinamool Congress denied him a ticket.
He was shot at in Badnabagram village area on July 21 last year and died two days later.