President Trump rescinded a pay raise Thursday for more than 2 million civilian federal employees next year, saying the government can’t afford the scheduled increases and issuing a call for a move to a merit-based pay system.

In a letter to Congress, Mr. Trump said a planned 2.1 percent across-the-board pay increase, and higher pay raises in some areas, instead will be set to zero on his orders. He said the move will save roughly $25 billion.

“We must maintain efforts to put our nation on a fiscally sustainable course, and federal agency budgets cannot sustain such increases,” Mr. Trump said.

Democratic lawmakers and the largest union representing federal employees reacted angrily, saying Republican tax cuts have drained far more revenue from the Treasury than the proposed pay raises would.

Sen. Patrick J. Leahy, Vermont Democrat and vice chairman of the Senate Appropriations Committee, suggested that lawmakers who approved a civilian pay raise of 1.9 percent this month by a vote of 96-2 would resist any House legislation that doesn’t include the pay raise.

“The Senate will continue to move forward on appropriations bills that have bipartisan support, that are at spending levels agreed to in the bipartisan budget deal, and that reject poison pill riders and controversial authorizing language,” Mr. Leahy said.

Sen. Mark R. Warner, a Virginia Democrat whose state is home to about 175,000 federal workers, called the president’s move “the latest attack in the Trump administration’s war on federal employees.”

“Congress can and must stand up to the president and reject this assault on our federal workers by passing the 1.9 percent pay raise that the Senate approved on Aug. 1,” Mr. Warner said.

The president’s move also could endanger the re-election bid of Rep. Barbara Comstock, a Republican whose Northern Virginia district includes thousands of federal workers. She said she opposes the president’s move.

“I strongly oppose eliminating the pay raise for civilian federal employees and will work with my colleagues to have the pay raise included in our appropriations,” Mrs. Comstock said. “Our public servants have been getting shortchanged for years, including three years of pay freezes under the Obama administration. Republicans recently made a strong statement in the House of Representatives supporting ICE and the work our dedicated homeland security officials do. We cannot 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.”

J. David Cox Sr., national president of the American Federation of Government Employees, said the Senate-approved pay raise for civilian employees is “the minimum that Congress should consider.”

“President Trump’s plan to freeze wages for these patriotic workers next year ignores the fact that they are worse off today financially than they were at the start of the decade,” Mr. Cox said. “Federal employees have had their pay and benefits cut by over $200 billion since 2011, and they are earning nearly 5 percent less today than they did at the start of the decade.”

Mr. Trump said federal law authorizes the president to implement “pay adjustments” in cases of national emergency or “serious economic conditions affecting the general welfare.”

“I view the increases that would otherwise take effect as inappropriate,” the president said.

The White House Office of Management and Budget has projected that the federal budget deficit will rise to slightly more than $1 trillion in fiscal 2019, an increase of $101 billion from the current year. The president came into office vowing to reduce budget deficits and the government’s total debt, which has climbed above $20 trillion.

But budget analysts say the biggest drivers of federal deficits are entitlement programs such as Social Security and Medicare. They add that these costs are rising and the White House and Congress haven’t addressed entitlement spending in any meaningful way.

In contrast to civilian employees, U.S. troops will receive a 2.6 percent pay increase, their largest in nine years. The military pay raise was authorized in a $716 billion defense bill that Mr. Trump signed into law this month.

In March, Mr. Trump reluctantly signed a $1.3 trillion spending bill that included the increase for defense spending. But he complained that Democrats added unnecessary spending and warned Congress that he would veto any similarly wasteful measures in the future.

The president said his decision to freeze pay rates “will not materially affect our ability to attract and retain a well‑qualified federal workforce.” He called for a shift to a system of merit pay.

“The cost of employing the federal workforce is significant,” Mr. Trump said. “In light of our nation’s fiscal situation, federal employee pay must be performance-based, and aligned strategically toward recruiting, retaining, and rewarding high-performing federal employees and those with critical skill sets.”

He said across-the-board pay increases and locality pay increases “have long-term fixed costs, yet fail to address existing pay disparities or target mission critical recruitment and retention goals.”

Under current law, “locality” pay increases averaging 25.70 percent would go into effect in January, in addition to a 2.1 percent across-the-board increase.

The left-leaning group VoteVets slammed Mr. Trump’s move, noting that about 30 percent of the federal workforce is made up of veterans. Spokesman Will Fischer said it is “simply obscene” to freeze pay after Republicans enacted broad corporate and personal income tax cuts.

“Our hardworking veterans sacrificed for this country, and at a time when wages are stagnant and inflation is on the horizon, it is simply cruel to cancel a pay raise that so many of these veterans in the workforce were depending on,” Mr. Fischer said. “It is simply a lie to say we don’t have the money. We do, but Donald Trump would much rather give it to his CEO buddies, for stock buybacks, than put it in the pockets of our workforce.”

Democratic National Committee spokesman Daniel Wessel called the move “another slap in the face to American workers.”

“Trump sent the deficit skyrocketing to give massive tax breaks to big corporations and the wealthiest Americans while working families got nothing,” Mr. Wessel said.

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