Ragesh Chandra (59), also the education secretary, had accompanied the chief minister to Delhi on Monday for meeting central ministers.
Chandra was found dead in his room at the Puducherry guest house in New Delhi, sources said.
They said his body has been shifted to AIIMS and would be brought here later this evening to enable government staff and others to pay their last respects.
A release from the office of the Chief Minister said the body would be airlifted from here to Kerala, his native place, tomorrow for last rites.
Chandra was due to retire in November this year. He had served Puducherry administration as a Civil Service Officer first and was conferred IAS in 2002.
Chandra is survived by wife and daughter.