Within 30 minutes of take-off from the Palam Technical Area, the aircraft developed a technical problem and returned to base, sources said.
The aircraft had reached Agra when the snag was detected.
President will now board another plane and resume the journey to Chennai to pay his last respects to Jayalalithaa.
Officials said it will take 40 minutes to one hour for the President to be air-borne again.
PTI