In the letter, Trump cited his authority in times of "national emergency or serious economic conditions affecting the general welfare" to make adjustments to the 2018 pay schedule for federal employees.
Under the previous plan, workers were scheduled for a 1.9 percent bump. Trump will use his authority to lower that to 1.4 percent.
"We must maintain efforts to put our Nation on a sustainable fiscal course," Trump wrote.
"A pay increase of this magnitude is not warranted, and Federal agency budgets could not accommodate such an increase while still maintaining support for key Federal priorities such as those that advance the safety and security of the American people."
Pay raises for government workers outside of Washington, D.C., will average only 0.5 percent and will be specified in a coming executive order, Trump said.
The White House did not respond to a question about how much the government would save from the action or whether it had discussed the matter with offices on Capitol Hill.
Trump will maintain the 2.1 percent pay increase for members of the military.
"I strongly support our men and women in uniform, who are the greatest fighting force in the world and the guardians of American freedom," Trump wrote.
"As our country continues to recover from serious economic conditions affecting the general welfare, we must work to rebuild our military's readiness and capabilities."