A deal which would have brought more international flights to the Northern Territory has fallen through, with Darwin Airport blaming its ongoing major runway works.

Sources have told the ABC that 18 months ago, Darwin Airport was close to landing a deal with Air Asia, which would have seen the low-cost carrier operate out of the NT capital.

But the deal never went ahead, with Air Asia pulling out after months of negotiations.

Darwin's Airport Development Group (ADG) executive general manager Rob Porter said the deal fell through because of what he described as "once in a generation" runway works.

"I think for all parties, it was a sensible decision to ensure that the services we put in here are profitable.

"New carriers coming to the territory during runway works was always going to be challenging."

Air Asia did not respond to requests for comment.

The carrier once operated out of Darwin, as did other international airlines including Garuda Indonesia, Malaysia Airlines and Donghai Airlines, none of which now service the NT.

Air Asia does run from Cairns, an equivalent international northern Australian airport in Queensland.

Earlier this week, Virgin Australia accused the ADG of charging high costs to airlines to land in Darwin, a situation which it said would "not incentivise airlines to grow services".

The ADG denied its fees were having an impact on airline competition and airfare costs.

Darwin's commercial international airport operates under a "joint user deed" with Australia's Defence Department, which has been driving the airport's runway works.

Last year, the runway works were blamed for a reduction in services, but Defence would not comment this week on whether the works were doing prolonged damage to the NT's economy.

In a statement, Defence said the runway works were a "normal part of airport operations".

"These critical airfield upgrades are essential for the safety of all aircraft and passengers, and will support projected air traffic volumes to at least 2040," a spokesperson said.

The works also come during a period when NT residents are facing sky-high flight prices, as well as unreliable flight scheduling and poor flight times.

Defence would not be drawn on whether the ongoing works were driving up flight prices.

"These are commercial decisions and there is no role for Defence in the shaping of those decisions," the spokesperson said.

Mr Porter pledged the runway works would be completed by mid-2025 and said the airport would then go back to carriers such as Air Asia "to see what their interest is in travelling to Darwin".