The official said EASA on Friday issued an emergency airworthiness directive for A320 neo planes fitted with PW1100 engines having a particular serial number.
This is the second problem affecting Pratt & Whitney GTF engines since the start of their marketing, the first causing delays in 2017 in delivery of the A320neo, the re-engined version of Airbus' single-aisle plane.
The issue is the latest in a string of problems that have bedeviled the GTF program.
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.
In a statement, IndiGo said it had proactively withdrawn the three A320 neo aircraft from service from February 9.
"We confirm receiving the recommendations by Pratt & Whitney as well as EASA (European Aviation Safety Regulator) with respect to the A320 neo aircraft powered by PW1100G - JM engines".
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As many as 11 of the 113 delivered Pratt-powered aircraft had been grounded, said informed source, with 43 in-service engines affected in total, all from the most recent batches to come off the engine maker's production line.
The EASA said that "several occurrences of inflight shutdown and rejected takeoff have been reported on certain" A320neo-family aircraft powered by GTF engines.
Airbus has also issued an alert for providing instructions to de-pair the affected engines and discontinue extended range twin-engine operations for aircraft fitted with affected engines. However, Indian LCC IndiGo confirmed it has grounded three A320neos after the EASA EAD was issued.
"We have identified the potentially affected engines and communicated with our customers", Pratt & Whitney said in a statement.
Earlier overheating problems on the Pratt engines have interfered with A320neo deliveries since early previous year.