The government originally planned 2.1 percent across-the-board increases and other adjustments based on the region of the country to take effect in 2019.
Washington has 75,525 people working for the federal government as of mid-2017, according to Governing.
"Accordingly, I have determined that it is appropriate to exercise my authority to set alternative across-the-board and locality pay adjustments for 2019". However, in the budget plan he released earlier this year, setting spending priorities for the coming year, Trump indicated he would seek a freeze on federal pay.
Members of the military are still set to receive a 2.6 percent pay hike.
Congress has an opportunity to effectively overrule the President's edict if lawmakers pass a spending bill that includes a federal pay raise.
"We can not balance the budget on the backs of our federal employees and I will work with my House and Senate colleagues to keep the pay increase in our appropriations measures that we vote on in September", she continued.More news: Playwright Neil Simon dies at 91
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Rep. Gerry Connolly, D-Va., who represents many federal workers, blamed what he said was Trump's mismanagement of federal government.
It would be the first pay freeze for civilian federal workers since 2011 to 2013, when President Barack Obama instituted a three-year pay freeze as the nation recovered from the recession.
In a letter to House and Senate leaders, Trump described the pay increase as "inappropriate".
Last year, Trump approved a 1.4 percent pay raise for federal employees.
"These numbers are very, very sustainable - this isn't a one-time shot", he said last month after figures showed the United States economy grew at a 4.1% annual rate in the second quarter of the year. It also issued a series of executive orders that would have made it all but impossible for federal employee unions to operate in federal buildings and to ease rules on firing employees. A federal judge invalidated numerous provisions in those executive orders on Saturday.
"Trump has delivered yet another slap in the face to American workers", said Democratic National Committee Chairman Tom Perez. "Today's announcement has nothing to do with making government more cost-efficient - it's just the latest attack in the Trump administration's war on federal employees". The president last year signed a package of tax cuts that is forecast to expand the deficit by about $1.5 trillion over 10 years.
U.S. District Judge Ketanji Brown Jackson said Trump didn't have the power to force changes to union contracts because they would violate the collective bargaining rights federal employees have under the law.