The Boeing aircraft owned by Air India were allowed to fly from New Delhi to Mumbai for maintenance reasons, said Arun Mishra, director general of India's civil aviation regulator.
"They did not carry any passengers, just two pilots were allowed inside each aircraft and we only gave them the permission to fly because the company was paying very high parking charges at the Delhi airport," said Mishra, declining to say when the flights were made.
Air India did not respond to calls by AFP.
Indian regulators had grounded Air India's six Dreamliner jets on January 17 in line with the US Federal Aviation Administration's advisory to cease flying the aircraft.
Aviation Minister Ajit Singh had demanded that US giant Boeing compensate the ailing Air India after the grounding order.
Air India and Boeing had earlier concluded negotiations for an undisclosed sum in compensation over a four-year delay in delivery of the Dreamliner to India because of production problems at the company.
Indian officials had said they were seeking up to $1 billion in compensation for the delays but neither side has disclosed whether the money has been paid.
Air India bought 27 Dreamliners as part of a 2005 multi-billion-dollar deal. It received the first plane last September and now has six, with the remaining 21 due to arrive by 2016.
Boeing's troubled next-generation model has suffered a series of glitches, although Boeing insists the plane is safe.
World regulators grounded all 50 operating Dreamliners after a fire aboard a parked Japan Airlines 787 on January 7 and a smoking battery that forced the emergency landing of an All Nippon Airways 787 on January 16.
Investigations continue into what caused the potentially catastrophic battery meltdown.