The regulator also asked IndiGo that all 97 such aircraft in its fleet must have modified PW engines by January 31 next year "at all costs".
The DGCA directive came after the airline faced four engine malfunctions in A320neo planes in the last one week, which "has caused serious concern and resultant disruption".
The Directorate General of Civil Aviation (DGCA) on Monday had asked IndiGo to replace 16 A320neo planes' PW engines, which have been used for more than 2900 hours, by November 12 but it found later that seven more aircraft are flying with such engines.
"Kindly note that after that none of these 23 aircraft, which does not have at least one LPT (low pressure turbine) modified engine on its wings, shall be allowed for commercial operation and their schedule will suitably be curtailed till this is accomplished," the DGCA said in a press note.
On Wednesday, one of the Pratt and Whitney engines of an IndiGo A320neo plane that was heading to Pune stalled mid-air, forcing the pilot to return to Kolkata.
On three consecutive days from October 24 to 26, IndiGo had three in-flight PW engine shutdowns, compelling the DGCA to visit the airlines' premises on Monday to review the maintenance and safety data.