"It is outrageous and hypocritical that after spending billions of taxpayer dollars on unnecessary tax cuts for the wealthy and big corporations ... that suddenly the White House finds that there is zero money left to pay a minimal cost-of living adjustment", he added.
Trump informed House and Senate leaders in a letter on Thursday.
That measure, along with a new two-year federal budget and tax cuts heralded by Republicans, have led to accusations Trump is ignoring the federal deficit, despite promising he would address it as president.
Trump put the cost of the raises associated with high-cost areas at $25 billion. That's wrong - and it disrespects the important work done throughout our country by federal workers. The Senate already cleared a 1.9 percent pay raise for civilian employees for next year.
The Trump administration proposed $143.5 billion in cuts to federal employee compensation in May, including substantial decreases in retirement funding.
Trump's call for a federal pay freeze was included in his budget proposal for 2019, the Office of Management and Budget said.
Unions representing the 2 million-member federal workforce urged Congress to pass the 1.9 percent pay raise.
"Federal employees have had their pay and benefits cut by over $200 billion since 2011, and they are earning almost 5 percent less today than they did at the start of the decade", said J. David Cox Sr., national president of the American Federation of Government Employees, the largest union representing federal workers.More news: Carabao Cup third round draw: Lampard comes up against Mourinho
Under President Barack Obama, federal pay was frozen between 2011 and 2013 as the economy recovered from the Great Recession, and no president has allowed full locality pay increases to take effect, according to Bloomberg. Congress will ultimately decide whether federal workers get a raise.
The president says that federal employee pay should be based on performance and should not involve fixed pay increases.
Trump announced Thursday he was nixing a 2.1% across-the-board raise for most workers effective in January, as well as separate locality pay increases averaging 25.7%. Accordingly, I have determined that it is appropriate to exercise my authority to set alternative across-the-board and locality pay adjustments for 2019 pursuant to 5 U.S.C. 5303 (b) and 5304a.
He said the 1.9 percent pay increase would "help prevent workers from falling further behind next year and help federal agencies recruit and retain the high-caliber workforce that the public expects and deserves".
"As noted in my budget for fiscal year 2019, the cost of employing the federal workforce is significant", he wrote.
In his letter, Trump stressed a pay freeze would not affect the federal government's ability to attract qualified workers, and wrote the government would focus on "recruiting, retaining and rewarding high-performing Federal employees and those with critical skill sets".
Instead of giving across-the-board increases, which he says don't address pay disparities or accomplish mission or retention goals, he wants to move to a merit-based system that rewards employees for their performance.