Previously, the airline had to get the engines by January 31.
In a statement, the aviation regulator said that post its order of November 1, 2019, the airline along with the aircraft and engine manufacturers have made significant efforts towards completion of the task.
"They have jointly and severally submitted a complete action plan, which finds the change of engines for the entire fleet feasible by the end of June 2020," it said.
It added: "However, DGCA feels that it can be compressed further and should be achievable by May 2020. And therefore, the revised timeline for complete removal of unmodified engines from the fleet is May 31 2020."
The regulator further noted that no aircraft with unmodified engine in Indigo fleet shall be allowed to fly after the extended deadline.
It said that one about 70 per cent of the total Neo engines of IndiGo's fleet is likely to be modified by January 31, 2020.
"Incidentally, the procurement of modified engines was adversely impacted due to holidays during Christmas and New Year at MRO (Maintenance, Repair and Overhaul) facilities," said the statement.
The budget airline witnessed around 13 incidents of engine trouble last year.
"Four Air Turn Back (ATB)/Inflight Shut Down (IFSD) events were witnessed on Airbus 320 Neo aircraft operated by M/s IndiGo in a week during October 2019 due to the failure of 3rd stage LPT blades, which caused serious concern."
At the root of the problem were the unmodified engines powering the IndiGo NeO fleet and the DGCA thereafter set up a timeline for change of these engines.
( With inputs from IANS )