The controversy stems from PeoplePlus, a new pay system that was put in place late last year. Some frustrated employees say they are getting paid too much, too little, or they are missing transit subsidies.
EPA officials said there are going to be bugs in any new system, but the process is improving.
"Every transition to a new information system requires fine-tuning, and EPA's transition to PeoplePlus is no exception," the agency said in a statement. "Our records show that salary payment errors in the system have amounted to fewer than 1 percent of total salary transactions, and the error rate is declining steadily."
The agency declined to discuss the issue beyond the statement.
EPA employees, meanwhile, described a very different situation.
"In New York, half the employees did not get their transit subsidies; other people are not getting their thrift savings contributions put in," said Paul M. Sacker, an EPA employee and the executive vice president of American Federation of Government Employees Council 238. "It seems to be ongoing, there doesn't seem to be any fix to it. We try to deal with the agency on it, and they just say, 'We're working on it, we're working on it.' "
Another New York City-based EPA employee, who asked not to be identified, said she never had problems under the old pay system. Under PeoplePlus, she says, her transit subsidy is regularly missing.
"I've been here almost two and a half years, and I've never had a problem before that," she said. "For me personally, it is kind of annoying ... it makes you wonder how long this is going to go on."
She also disputed the agency's characterization that problems with the system are isolated.
"Most people don't like it," she said. "They have one problem or another."
Sacker said EPA is using a "faulty software package."
"We don't think the senior management is taking it this seriously," Sacker said. "I mean, it's the federal government. You're supposed to get your paycheck on time."