The Department of Transportation on Thursday refused to allow JetBlue and Spirit airlines to end service to dozens of cities as they seek to slash costs during the coronavirus pandemic, issuing its first decisions on a key provision of the federal bailout of the industry.

The $2 trillion stimulus bill, signed by President Trump last month, set aside some $50 billion to help airlines, but the money comes with strings attached: The carriers had to agree not to lay off workers and to maintain at least minimal service to cities they were serving at the beginning of March.

The Transportation Department ruled that airlines could pare service significantly, but at least 10 airlines have asked the government for waivers so they can cut further still.

JetBlue and Spirit, the first to file their requests, argued that they should be allowed to close down operations at three dozen airports to save money when there’s no demand for flights.

Low-cost carriers in particular have argued they don’t play a as vital a role during the crisis because they aren’t shipping medical supplies or carrying business travelers.

But the Transportation Department said Thursday it didn’t find the two airlines’ arguments compelling, saying in a written decision that they had “not persuaded the Department that we must strike a different balance.”

The stimulus legislation, known as the Cares Act, singled out the aviation system for billions of dollars in aid as would-be travelers have been ordered to stay home and canceled tickets. Daily passenger numbers have dropped to about 100,000 from around 2.5 million.

Half of the federal money was to be grants to airlines to maintain their payrolls, a provision strongly favored by unions. But in the deal finalized this week with 10 airlines, the carriers agreed to pay back 30 percent of the money and to let the government acquire stock as a way for the government to recoup some of taxpayers’ outlay.

The interpretation of the minimum service requirement has been similarly contentious, with some communities fearing losing critical air links and lawmakers seeking to intercede with the Transportation Department for more favorable terms. Airlines, meanwhile, have said operating even a few flights means taking to the skies with next to no passengers, burning money at a time when no revenue is coming in.

“Spirit, like other airlines, is in survival mode which has necessitated temporarily discontinuing service to the cities,” the airline wrote in its application for a waiver.

JetBlue argued that granting its request would ensure the airline was positioned to bounce back once the pandemic has passed.

“A rigid interpretation of the Service Obligation will only threaten to unnecessarily diminish JetBlue’s liquidity, with no commensurate public interest benefit,” the airline wrote.

Spirit, the most high-profile airline to not yet have reached an agreement on the payroll grant money, included at least two dozen cities on its list. Among them were Richmond; Sacramento; and Latrobe, Pa., which the airline characterized as neither “small or remote.”

Even if those communities were not served by the airline, travelers would “continue to have good access to air transportation,” Spirit wrote.

On March 30, Spirit became the first airline to cancel all flights to New York, New Jersey and Connecticut. In announcing the decision, the carrier said it was following warnings against all nonessential travel to the region that were put out by the Centers for Disease Control and Prevention.

JetBlue singled out 11 airports for cuts, but promised to restore service “as soon as it is both safe to do so and when even the slightest customer demand re-emerges.”

The airline said that it had polled officials at the airports and found that they would accept the cuts.

In interviews, officials at some of the airports on Spirit and JetBlue’s proposed list of cuts said they were not worried about losing the service because they had ample connections from mainline carriers.

“We’re really partners with the airlines and we understand their situation is very, very much tied to ours,” said Brian Sprenger, director of Bozeman Yellowstone International Airport.

Sprenger, whose airport is on JetBlue’s list of proposed cuts, said he is seeing 5 to 10 percent of typical passenger numbers.

“We don’t want them flying around empty airplanes just for the sake of it,” he said.

The Transportation Department did agree to allow the airlines to end service to some airports in Puerto Rico, where the governor has directed flights to a single airport so passengers can be screened, and acknowledged it had erroneously required Spirit to serve three cities where it did not actually operate routes. But otherwise, it turned the carriers down.

The department’s order on minimum service levels does not require airlines to serve every airport they had previously flown to, merely the same cities. That provision has provoked complaints from members of Congress who represent areas served by a mix of different size airports.

Sen. Jeanne Shaheen (D-N.H.) wrote to the department saying she was concerned that airports like the one in Manchester, which is considered part of the Boston area, could suffer in the long term. Similar concerns were raised by a bipartisan group of members of Congress from Southern California.

Sens. Tim Kaine (D) and Mark R. Warner (D) of Virginia and a trio of House members wrote to the department last week asking it to reconsider its decision to lump together Newport News and Norfolk. They argued that the two cities, separated by a body of water, are difficult to drive between and that the military facilities of the Peninsula, and Newport News Shipbuilding, which builds aircraft carriers, deserved special consideration.

“A potential hiatus in air carrier operations as a result of the Department’s proposed parameters for the implementation of the CARES Act threatens to negatively affect these critical national security operations,” they wrote.