Airbus brought the issue to the European aviation agency's attention, a spokesperson said, and the company has outlined safety recommendations for airlines until Pratt & Whitney can fix or replace the engines.
Technical issues with certain engines of IndiGo's A320neo planes had led to the grounding of many flights previous year.
The issue is the latest in a string of problems that have bedeviled the GTF program.
The Directorate General of Civil Aviationofficial said IndiGo has three such aircraft, which have been grounded.
European Aviation Safety Agency (EASA) had issued a emergency airworthiness directive (EAD) on Feb 9, that warns even possibility of dual engine in-flight shut-down.
Pratt spent billions to develop the new geared engines and some issues are common, but that has meant severe headaches for Airbus and its airline customers.
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Its customers have also become less forgiving about performance standards as schedules tighten and airlines squeeze more flight hours out of their aircraft.
The issue impacts a limited sub-population of engines and IndiGo had to ground three of its aircraft in the interim, it added. Both A320neos and A321neos are affected.
According to the filing, IndiGo would continue to add A320 ceo and ATR aircraft to its fleet. Aircraft with one affected engine are restricted from certain extended-range flights.
"As a precaution, aircraft with these engines will be addressed in a manner consistent with the operational instructions issued by Airbus, and coordinated between Airbus and Pratt & Whitney as needed". "The aircraft have been grounded for technical reasons", the spokesperson said.
Airbus said in a statement that Pratt is "investigating the root cause of this new finding with the full support of Airbus".