Agency chief James Loy signed an order precluding collective bargaining by any screeners, saying the law creating the agency in November 2001 gave him the authority to do so.
Loy is concerned that a labor contract could hinder efforts to quickly make staffing changes in response to a terrorism threat, said his spokesman, Robert Johnson.
"When it comes to responding to new intelligence or terrorist threats on a moment's notice, we don't have time to check with a shop steward," Johnson said.
Federation spokeswoman Diane Witiak said the union has received thousands of complaints from agency workers and intends to press forward with its organizing.
"We're not abandoning these employees," she said. "We're going to continue our organizing campaign."
Collective bargaining rights were a major issue in the debate over creating the Homeland Security Department. Congress decided to let the president strip collective bargaining rights from department workers, though that decision would be revisited every four years.
Sen. Edward M. Kennedy, D-Mass., said the administration already has the authority to suspend collective bargaining rights during a true national emergency.
"It's not homeland security, it's union busting," Kennedy said in a statement.
Witiak said workers have been forced to work 21-hour shifts and paychecks have been delayed by a month. She also claimed some workers have been sexually harassed and that employees want to be issued protective equipment when searching baggage for explosives.
Johnson acknowledged some screeners' paychecks were delayed because of paperwork problems caused by the rapid hiring of 23,000 baggage screeners and 33,000 passenger screeners in less than a year. The agency is working to pay all workers quickly.
He said the agency will not stand for sexual harassment, and long hours and sudden shift changes will become less of an issue as agency operations become more routine. The agency hired all its workers in a year and scrambled to meet deadlines to check each passenger and every checked bag.
"Getting this agency running in less than a year, and meeting the deadlines that were laid out in the law, has required a lot of people to work long hours," Johnson said.
The union has petitioned the Federal Labor Relations Authority for elections on collective bargaining by workers at Pittsburgh International and Chicago Midway airports and plans to file several more petitions soon, Witiak said. The union has to organize at each airport individually.
The agency was created in response to the Sept. 11 attacks. Congress gave it authority to oversee airport security, which had been run by airlines that hired private companies. Critics said the companies offered little pay or training and few benefits, leading to high turnover and poor job performance.
The screeners earn between $23,600 to $35,400 a year, with health care, life insurance, paid vacation and sick leave. Before Sept. 11, the private-sector screeners generally earned minimum wage, or around $10,000 a year, and often received no benefits.
On the Net: Transportation Security Administration: www.tsa.gov American Federation of Government Employees: www.afge.org