"That can mean changes in work assignments and other conditions of employment that are not compatible with the duty to bargain with labor unions," he said.
The admiral's order appeared to be an important early test of the Bush administration's demand that federal employees working in the nascent Department of Homeland Security be denied certain job protections in the interest of government flexibility.
It came as workers at New York's La Guardia Airport, Baltimore- Washington International Airport, Pittsburgh International Airport and Midway Airport in Chicago petitioned the Federal Labor Relations Authority to open the way for the formation of local union chapters of the American Federation of Government Employees to represent them.
Bobby L. Harnage Sr., the union's national president, said the administration was merely imposing its anti-union agenda.
"Admiral Loy surely knows that the administration already has the flexibility to suspend collective bargaining during a true national emergency," Mr. Harnage said. "The Bush administration has shown once again that the war it cares about most is the one it is waging against the U.S. government work force."
In the last year, Admiral Loy's new agency has hired, trained and deployed more than 60,000 airport screeners of baggage and people. Over the objections of the administration, Congress required that the workers be federal employees based on the expectation that they would be more conscientious.
Union officials said some workers were being asked to work extended shifts and have had their paychecks delayed by as long as a month.
Tom Daschle, the Senate minority leader, called the administration's order "shameful but not surprising."
"To say that the workers tasked with our safety don't have the right to bargain collectively on issues like their own safety has nothing to do with America's security and everything to do with this administration's politics," Mr. Daschle said.