Air Deccan has threatened to move its current base from Maharashtra to Gujarat, owing to aircraft parking and slot issues.
The scheduled commuter airline, which is now owned by Ahmedabad-based firms - GSEC Aviation and Monarch Networth Capital - had launched its services in the state last year.
At present, it parks its aircraft at HAL-run Nashik Airport due to a space crunch at Mumbai airport.
"Flights under Udan are increasingly becoming unviable for us in Maharashtra as we are not getting the right slots besides aircraft parking space," said Shaishav Shah, managing director, Air Deccan.
"This may force us to move our base to Ahmedabad, where availability of parking space is not an issue," Shah said.
Air Deccan had bagged 34 routes, including those in Maharashtra, in the the first phase of bidding for the government's Ude Desh ka Aam Nagrik (Udan) regional connectivity scheme in March 2016.
Besides, Air Deccan, the two firms also own 60 per cent stake in another scheduled commuter airline Air Odisha.
Air Deccan launched its maiden services in Maharashtra, with a flight to Jalgaon from Mumbai last December and later extended the network to Kolhapur, Pune and Nashik.
The airline was, however, forced to suspend its operations to these destinations due to "pilots and aircraft" issues but subsequently resumed it in July.
"From Ahmedabad, we will fly to Nashik and then to Mumbai. From Mumbai, we can do our Udan network and come back to Ahmedabad base," Shah added.
He said that Air Deccan has requested to change its slot timings at the GVK-run Mumbai airport to 9.20 am and 9.50 am instead of 6.50 am and 7.40 am but the aerodrome operator has not paid heed to its request.
A query sent to Mumbai International Airport on the issue remained unanswered.
Alleging harassment by Nashik airport authorities, Shah said that the airport operators was not providing the parking space and raising "illegal" bills against the carrier for availing certain services.
"The illegal bill as referred by Air Deccan pertains to the various services provided by HAL airport at Ozar for non-RCS route (Nashik-Mumbai-Nashik) such as landing charges, parking charges, allied services, Terminal navigation and landing charges, extension of watch hours, X-Ray and passenger service fee," HAL spokesperson said in a statement to PTI.
Both Air Deccan and Airport Authority of India have confirmed this, it said adding, "Air Deccan is fully aware of the charges involved for such type of activities as bills in respect of non-RCS flights from Nashik airport were paid by them in the past."
"The question of harassment by HAL authority does not arise," the spokesperson added in the statement.