They are also worried about how many employees will lose their jobs as Congress and the president struggle to deal with the budget deficit, CNNMoney reported Friday.
Colleen M. Kelley, president of the National Treasury Employees Union, said union members believe Obama "has stood with federal employees 90 percent of the time."
Unions had supported Obama even though earlier this year he announced the pay freeze would be extended through March 2013, when workers would get a 0.5 percent increase.
While Kelley said she expects the Congress to attempt to cut federal pay and benefits, her primary issue now is getting salaries for federal workers unfrozen by Jan. 1.
If Congress fails to act on the deficit by Jan. 1, federal programs face $1.2 trillion in spending cuts over the next 10 years, and 277,000 workers could lose their jobs in the next 12 months, the Center for Regional Analysis at George Mason University found in a study.