Batcha, who was under the CBI scanner, was found hanging at his house here on March 16 with his wife claiming that he had committed suicide "unable to cope with the 2G probe."
The Directorate of Public Health has reportedly rejected Dr V Dekal's resignation on grounds of shortage of staff and that he did not provide sufficient notice.
However, Dekal said that he was only on contract with the Health Department and could, therefore, quit any time.
He had requested to be relieved from service to contest the April 13 Tamil Nadu Assembly polls and had put in his papers in the first week of March.
Dekal had last week moved the High Court seeking a direction to consider his resignation since no action had been taken by the authorities concerned.
The court had directed the Director of Public Health to consider the resignation and pass orders in accordance with law.
After the autopsy, Dr Dekal had said that 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.
38-year-old Batcha was Managing Director of Greenhouse Promoters, a firm under the scanner of CBI and Enforcement Directorate in connection with the 2G spectrum scam.
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.