The Directorate General of Civil Aviation (DGCA) has ordered Air India to sack three senior managers responsible for crew scheduling after the breaches, according to official reports seen by Reuters.
A divisional vice president, a chief manager of crew scheduling, and a planning executive have all been removed on the DGCA's orders.
The flights in question, which took off on 16 and 17 May, exceeded the 10-hour limit on pilots' flying time, the report revealed.
Investigators cited "systemic failures in scheduling protocol and oversights" and hit out at the lack of proper disciplinary action against those involved.
This safety issue is unrelated to this month's Air India crash that claimed 241 lives.
The tragic incident happened on Thursday, 12 June, when an Air India Boeing 787-8, carrying 53 Britons, crashed shortly after take-off from Ahmedabad airport in western India.
A full investigation into the cause of the crash is still ongoing.
Earlier this week, Air India was also warned for breaches after three of its Airbus planes flew despite being overdue safety checks on emergency escape slide equipment.
In response to the regulator's latest order, Air India told Reuters: "We have implemented the DGCA order and, in the interim, our chief operations officer will directly oversee the Integrated Operations Control Centre.

"Air India is committed to ensuring that there is total adherence to safety protocols and standard practices."
The DGCA noted that Air India had voluntarily disclosed these violations.
Last year, around half of the fines handed out by India's aviation watchdog were given to Air India or its subsidiary, Air India Express.
The largest penalty was $127,000 (£94,370) for "insufficient oxygen on board" some of its international flights.
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