"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.
In a notice to Congress Thursday, Trump cited "serious economic conditions" in cutting pay to civilian workers.
Federal workers were to get a 2.1 percent across-the-board raise in January, with more for those who live in high-cost areas.
"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 deemed both "inappropriate". 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.
Congress has an opportunity to effectively overrule the President's edict if lawmakers pass a spending bill that includes a federal pay raise.
Trump's 2019 budget proposal sought to freeze federal pay, but the Senate Appropriations Committee included a pay bump in its spending plans for 2019.
Trump is not anxious about the effect of freezing federal pay on the government's ability to be successful in "recruiting, retaining and rewarding high-performing Federal employees and those with critical skill sets".
"We must maintain efforts to put our Nation on a fiscally sustainable course, and Federal agency budgets can not sustain such increases", Trump wrote in a letter to House Speaker Paul Ryan and Senate Majority Leader Mitch McConnell.
The Trump administration proposed $143.5 billion in cuts to federal employee compensation in May, including substantial decreases in retirement funding. "We must maintain efforts to put our Nation on a fiscally sustainable course, and Federal agency budgets can not sustain such increases".
"Accordingly, I have determined that it is appropriate to exercise my authority to set alternative across-the-board and locality pay adjustments for 2019".
Trump's decision does not affect pay for military personnel; instead, US troops are due a 2.6 percent pay increase next year.
Trump said the pay freeze "will not materially affect our ability to attract and retain a well-qualified Federal workforce".
As noted in my Budget for Fiscal Year 2019, the cost of employing the Federal workforce is significant.
Trump explained the move in terms of the national debt, now more than $21 trillion, and the annual deficit, expected to be $804 billion in fiscal 2018.