The issue will now come up for hearing on July 21.
A bench headed by Chief Justice of India K G Balakrishnan backed the Director General of Civil Aviation's (DGCA) circular, which had brought 1992 rules regarding pilots' duty hours back into force.
The DGCA circular had proposed increasing the duty hours of pilots and cabin crew.
The apex court in its direction asked the pilots to go for three flights in nine hours in accordance with the DGCA guidelines.
On July 1, the Bombay High Court stayed the DGCA's circular and asked it to restore the 2007 rules of flight duty hours and timings.