The civil aviation ministry had mooted the idea because of slot constraints at the Indira Gandhi International (IGI) Airport.
According to an agreement between Delhi International Airport Limited (DIAL), a consortium led by GMR Group, and the government, commercial flight operations from an airport within 150 kms of the IGI Airport are not allowed.
"DIAL has agreed with the Ministry of Civil Aviation's proposal," a GMR spokesperson wrote in response to an e-mail query.
"Use of Hindon Air Force Station will only be a temporary and stop-gap arrangement for the limited purpose of operating flights and networks awarded under RCS. This arrangement is only till the time DIAL completes the expansion and upgradation of facilities at IGI Airport," the spokesperson added.
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All RCS flights will have to be shifted back to the IGI Airport on the completion of upgradation work.
An airport official said that there was no clarity at the moment on whether all future RCS flights from Delhi would be operated from Hindon or only some of them would be shifted to the IAF base.
Five airlines were awarded a total of 128 routes during the first round of bidding for RCS. The second round of bidding began in August.
Airlines receive a subsidy from the Centre and the state government for setting aside half their seating capacity at discounted rates.
Civil Aviation Secretary R N Choubey had last month said that the IAF had already given consent to the use of its airbase in Ghaziabad, on the outskirts of Delhi, for commercial purposes.
As part of the agreement, the type of planes which can be operated for RCS flights from Hindon will be those with a seating capacity of not more than 80 seats.
The GMR spokesperson also wrote that the consent given by DIAL is a "one-off case" and should not be construed as a "pre-cursor" for any other RCS airports within 150 km of the IGI Airport.
The busiest in the country, the Delhi airport sees 67 air traffic movements (departures and arrivals) per hour, which goes up to 72 during peak hours.