Justice N Paul Vasanthakumar, before whom the petition came up, directed the Director of Public Health to consider the resignation and pass orders in accordance with law.
The order should be communicated on or before Mar 24, the judge said. Batcha's body was found hanging in his house in South Chennai on Wednesday last.
After the autopsy, Dr Dekal had said Batcha's death was due to asphyxia and his body showed compression of the neck with hanging mark and that the cause of death cannot be confirmed till the forensic report was received.
Dr Dekal, who put in his papers in the first week of March, said his resignation has nothing to do with the case as he planned to contest the Apr 13 assembly elections.
He filed a petition on March 12, saying he had submitted his resignation on Mar 3 in order to contest the poll.
He said he filed a petition seeking a direction to consider his resignation to relieve him at the earliest since no action had been taken by the authorities concerned.
Thirty eight-year-old Batcha, who was Managing Director of Greenhouse Promoters, a firm under the scanner of CBI and Enforcement Directorate in connection with the 2G spectrum scam, was found hanging in his house in South Chennai.
Batcha, whose official and residential premises were raided by CBI and who was questioned at least four times in the last two months, had left a suicide note in which he had stated he was "embarrassed" by the raids and the extensive media coverage.