WASHINGTON — President Trump continued his purge of inspectors general late Friday, moving to oust Steve A. Linick, who had served in that post at the State Department since 2013, and replacing him with an ambassador with close ties to Vice President Mike Pence.

Mr. Linick, who was named by President Barack Obama to lead the office of the inspector general at the State Department, will be replaced by Ambassador Stephen J. Akard, the director of the Office of Foreign Missions, the State Department said in a statement on Friday night.

In a letter to Speaker Nancy Pelosi that was obtained by The New York Times, Mr. Trump wrote that “it is vital that I have the fullest confidence in the appointees serving as Inspectors General.”

“That is no longer the case with regard to this Inspector General,” the president added.

The decision to remove Mr. Linick, first reported Friday night by Politico, is the latest in a purge of inspectors general whom Mr. Trump has deemed insufficiently loyal to his administration, upending the traditional independence of the internal watchdog agencies whose missions are to conduct oversight of the nation’s sprawling bureaucracy.

On May 1, even as the coronavirus pandemic continued to ravage the country, Mr. Trump moved to oust Christi A. Grimm, the principal deputy inspector general for the Department of Health and Human Services, whose office had issued a report revealing the dire state of the nation’s response to the pathogen.

A month earlier, the president ousted Michael K. Atkinson, the inspector general of the intelligence community, telling the leaders of two congressional committees that he had lost confidence in him. Mr. Atkinson had infuriated the president by insisting on telling Congress about the whistle-blower complaint that prompted the impeachment inquiry into Mr. Trump’s dealings with Ukraine.

The president also took steps to remove Glenn A. Fine, who has been the acting inspector general for the Defense Department since before Mr. Trump took office, so that he could not be installed as the leader of an oversight panel intended to keep tabs on how the Trump administration spends trillions of dollars in pandemic relief approved by Congress.

Under law, the administration must notify Congress 30 days before formally terminating an inspector general. Mr. Linick is expected to leave his post then.

The removals of the inspectors general — and their replacements by allies of the president’s — are part of an aggressive move by Mr. Trump and his top aides against who he considers to be “deep state” officials in many key agencies and who he believes are opposed to his agenda.

That effort accelerated in the weeks after the president was acquitted in a Senate impeachment trial. Mr. Trump viewed the inquiry into his actions related to Ukraine as a “coup” orchestrated by career officials and Democratic politicians determined to bring his presidency to an early conclusion.

Ms. Pelosi, who led the impeachment effort in the House, condemned the move late Friday to replace Mr. Linick.

“The late-night, weekend firing of State Department IG Steve Linick is an acceleration of the President’s dangerous pattern of retaliation against the patriotic public servants charged with conducting oversight on behalf of the American people,” she said in a statement on Twitter.

Representative Eliot L. Engel, Democrat of New York and the chairman of the House Committee on Foreign Affairs, called the decision to remove Mr. Linick an “outrageous act” meant to protect Secretary of State Mike Pompeo from accountability.

Representative Joaquin Castro, Democrat of Texas and the chairman of the Oversight and Investigations Subcommittee of the Foreign Affairs Committee, said on Twitter that the move by the White House was a “potential cover up” by Mr. Trump and Mr. Pompeo, and that it could result in a congressional inquiry.

“Congress & @HouseForeign Oversight Subcommittee will hold the Trump admin accountable for any illegal actions and corrupt conduct,” Mr. Castro tweeted.

In his statement, Mr. Engel said that he had learned that Mr. Linick’s office had opened an investigation into Mr. Pompeo. Mr. Engel said that “Mr. Linick’s firing amid such a probe strongly suggests that this is an unlawful act of retaliation.”

Mr. Engel did not offer any more details, but a Democratic aide said that Mr. Linick was looking into whether Mr. Pompeo had misused a political appointee at the State Department to perform personal tasks for himself and his wife.

A spokeswoman for Mr. Pompeo did not immediately respond to an email seeking comment about the accusation.

Mr. Linick was a bit player in the impeachment inquiry, briefly drawing attention to himself at the height of the investigation into Mr. Trump’s actions. In October, he hand-delivered a packet of information to congressional investigators, saying he thought it might help answer whether the president pressured Ukraine to investigate former Vice President Joseph R. Biden Jr. and his son Hunter Biden.

In the end, the roughly 40 pages of material turned out to be largely inconsequential: a record of contacts between Rudolph W. Giuliani, the president’s personal lawyer, and Ukrainian prosecutors, as well as accounts of Ukrainian law enforcement proceedings.

At least two investigations by Mr. Linick’s office have caused friction with senior political appointees at the State Department.

In November, the office said it had found that appointees at the agency, when it was led by Secretary of State Rex W. Tillerson, had retaliated against an Iranian-American career civil servant because of her ethnicity and a perception that she held political views different from those of top Trump officials. Brian H. Hook, then the head of the office of policy planning, where the career official, Sahar Nowrouzzadeh, worked, was scrutinized in that inquiry. Mr. Hook is now the special representative for Iran and works closely with Mr. Pompeo.

In August, Mr. Linick’s office found that two political appointees in the Bureau of International Organization Affairs — the assistant secretary Kevin Moley and his senior adviser Mari Stull — had harassed career employees. Mr. Pompeo did not fire Mr. Moley, who announced in October he would retire later that year.

Employees of the State Department’s inspector general’s office have viewed Mr. Linick as a competent, nonpartisan leader.

Mr. Akard, by contrast, has been a controversial figure since his nomination for a senior State Department job when Mr. Tillerson was secretary. The White House had pushed Mr. Akard for the job of director general of the Foreign Service, a top management position that has traditionally gone to a respected career official with decades of experience.

A close associate of Mr. Pence’s, Mr. Akard had served as the director of international development at the Indiana Economic Development Corp., in the state where Mr. Pence once was governor. Members of Congress heard the intense grumblings of longtime State Department employees and signaled to the White House in 2018 that he would not be confirmed; even senior Republicans had opposed the nomination.

In 2019, Mr. Akard was confirmed as the department’s director of the office of foreign missions, a job with the rank of ambassador that top career officials do not consider meaningful compared with the director general post.

Michael D. Shear reported from Washington, and Maggie Haberman from New York. Edward Wong and Catie Edmondson contributed reporting from Washington.