The Treasury will also receive stock warrants worth 10 percent of the loan amount that exceeds $100 million.

The official said that the structure of the agreement was a carefully negotiated compromise, as airlines were seeking grants with no repayment and the administration preferred loans. The economic relief legislation also allocated a separate $25 billion specifically for loans to the airlines, but the official said that negotiations with the companies for those funds had not begun. The Treasury is also engaged in negotiations with cargo carriers, which are eligible for $8 billion in grants and loans.

The Treasury Department said last week that it would not require airlines that receive up to $100 million in bailout money to give the government equity stakes or other compensation. The government had received over 200 applications from U.S. airlines seeking payroll support and the Treasury said the majority of those were asking for less than $10 million.

Airlines that accept the payroll support money are prohibited from major staffing or pay cuts through September. The airlines must also refrain from buying back shares or paying dividends through September 2021 and must agree to limits on executive pay until late March 2022.

In a statement, Sara Nelson, the president of the Association of Flight Attendants union, welcomed the payout as “an unprecedented accomplishment,” but criticized Mr. Mnuchin for delaying the aid and for asking that airlines repay a portion of the funds.

“Now we must fight to keep aviation intact to protect our industry and ensure our economy lifts off again when the virus is under control,” Ms. Nelson said. “We have seen what happens when investment bankers like Secretary Mnuchin control the outcomes, and we will not stand by to watch it play out again.”

Separately, Capt. Joe DePete, the president of the Air Line Pilots Association, which represents more than 63,000 pilots at United, Delta and other airlines, accused the department of “undermining the intent” of the law, “which will make it harder to stop layoffs and slow the recovery.”