Obama said in a letter to House Speaker John Boehner, R-Ohio, that the decision to extend the two-year pay freeze shouldn't hamper the government's ability to hire good employees, CNN reported.
"This decision will not materially affect the federal government's ability to attract and retain a well-qualified federal workforce," Obama said in the letter.
Congressional leaders struck a budget deal to fund the federal government for six months but didn't pass it before the August recess. The government's 2013 fiscal year begins Oct. 1.
Obama and Congress have frozen federal employees' pay during the last two years. Obama has said any pay raise should wait until after Congress passes a budget to funding government agencies through the first six months of the new fiscal year.
While Obama could have used his authority to raise federal salaries by 1.5 percent, he settled on a 0.5 percent increase instead, saying in his letter, "we must maintain efforts to keep our nation on a sustainable course."
Several union organizations expressed disappointment that Obama planned to extend the pay freeze especially since he called for the freeze to be lifted in his budget proposal, CNN reported.
"We are surprised and deeply disappointed by the administration's decision not to push for the modest federal pay adjustment that was called for in the president's budget," William Dougan, National Federation of Federal Employees president, said in a statement.
Trader Joe's: Car crashes into Long Island store, injuring 11
Exploding whale video goes viral on Internet