WASHINGTON — The State Department’s acting watchdog has resigned from his post less than three months after replacing the previous inspector general, whom President Trump fired in May, the department said on Wednesday.The departure of Stephen J. Akard came as Congress continued to investigate the firing of his predecessor, Steve A. Linick, who was pursuing inquiries into Secretary of State Mike Pompeo. Three congressional committees issued subpoenas this week to top aides of Mr. Pompeo.Mr. Linick had opened investigations into Mr. Pompeo’s potential misuse of department resources and his effort to push arms sales to Saudi Arabia and the United Arab Emirates.The department gave no explanation for the departure of Mr. Akard, an ally of Vice President Mike Pence. A department spokeswoman said Mr. Akard, who is from Indiana, would be “returning to the private sector,” and the deputy inspector general, Diana R. Shaw, would take over as acting inspector general.Mr. Akard “left to go back home,” Mr. Pompeo said at a news conference on Wednesday. “This happens. I don’t have anything more to add to that.”The departure is yet another disruption to the State Department’s internal watchdog office, where hundreds of employees investigate fraud and waste.Mr. Akard took over the acting inspector general role after Mr. Linick, who was appointed to the post by President Barack Obama in 2013, was fired by Mr. Trump in mid-May at the private urging of Mr. Pompeo. Mr. Linick was known to be cautious and nonpartisan.The events surrounding Mr. Linick’s removal have come under intense scrutiny. Three congressional committees are investigating Mr. Pompeo’s role in the events. Mr. Pompeo has said Mr. Linick was “undermining” the work of the State Department, though he has given no details.On Monday, lawmakers subpoenaed four State Department officials to further their investigation.Two of the aides, Brian Bulatao and Toni Porter, are longtime close friends of Mr. Pompeo and his wife, Susan. They were appointed to senior roles by Mr. Pompeo at both the State Department and the C.I.A., where Mr. Pompeo served as the director for one year.The other two are Marik String, the agency’s acting legal adviser, and Michael Miller, the deputy assistant secretary of state for political and military affairs. Lawmakers and aides intend to question them about their actions and those of Mr. Pompeo in pushing through the arms sales, as well as Mr. Linick’s inquiry into the issue.“The administration continues to cover up the real reasons for Mr. Linick’s firing by stonewalling the committees’ investigation and refusing to engage in good faith,” Democratic leaders of the committees wrote on Monday. “That stonewalling has made today’s subpoenas necessary.”Mr. Akard’s appointment as acting inspector general was met with skepticism. It prompted critics to wonder if it was an effort to politicize an office meant to be an independent internal unit.In addition to serving as the State Department’s acting watchdog, Mr. Akard was also the agency’s ambassador-level head of the Office of Foreign Missions, an arrangement that was a clear conflict of interest and widely criticized by Democratic lawmakers.Mr. Akard worked as the chief of staff of the Indiana Economic Development Corporation when Mr. Pence was the governor of the state.After taking on the acting watchdog role at the State Department, Mr. Akard told officials there that he would recuse himself from the ongoing inquiries into Mr. Pompeo and his wife’s potential misuse of government resources and into the arm sales. He also pledged to recuse himself from any inquiry involving the office he oversaw, according to a letter he sent to House lawmakers in June.The office was also investigating Robert Wood Johnson IV, the United States ambassador to Britain and a close ally of Mr. Trump, over accusations that he had made racist and sexist remarks to embassy staff.Senator Bob Menendez of New Jersey, the lead Democrat on the Foreign Relations Committee, expressed concern after hearing of Mr. Akard’s resignation, which was first reported by The Washington Post and CNN.“Independent, experienced inspectors general are paramount to effective oversight,” Mr. Menendez said in a statement. “I do not believe he was the right choice to lead the office, but I am concerned that his sudden resignation leaves another opportunity for the Trump administration to try to weaken oversight and accountability.”Representatives Eliot L. Engel and Carolyn B. Maloney, both Democrats of New York who are leading the two House committees investigating the Linick firing, said in a joint statement that Mr. Akard’s resignation “must not further disrupt the Office of Inspector General’s important investigations. Any effort by the Trump administration to install another political loyalist would further undercut the ability of the office to properly carry out its critical mission.”Critics have said that Mr. Pompeo urged Mr. Trump to fire Mr. Linick out of retribution and to evade accountability.Mr. Pompeo has admitted that he knew about at least one of Mr. Linick’s investigations, a nearly completed inquiry into whether Mr. Pompeo had acted unlawfully in bypassing Congress to push through $8.1 billion of arms sales to Saudi Arabia and the United Arab Emirates last year. During a review process, senior lawmakers from both parties had put a freeze on the sales, but Mr. Pompeo declared an “emergency” in May 2019 to do an end run around the congressional hold, citing Iran’s actions in the Middle East as justification. Lawmakers asked Mr. Linick the next month to open an investigation into the legality of Mr. Pompeo’s action.This June, Mr. Linick testified in Congress that Mr. Bulatao, the under secretary of state for management, tried to “bully” him as he conducted his examination into the potentially illegal action.Aides to Mr. Linick briefed a handful of State Department officials on the report’s preliminary findings in early March, and officials there and in Congress expect the report to be issued. It is unclear what role Mr. Akard has played in the investigation since he replaced Mr. Linick in May.Arms sales to Saudi Arabia and the United Arab Emirates, which are accused of vast human rights violations and helping kill thousands of civilians in the Yemeni civil war, have been one of the biggest points of contention between the Trump administration and Congress.Mr. Trump and aides in the White House have been strong proponents of the sales. Frustrated that lawmakers continue to put holds on proposed sales, senior administration officials are considering trying to end the decades-old congressional informal review process.The three congressional committees investigating Mr. Linick’s firing said on Monday that the voluntary testimony last week of Charles Faulkner, a former State Department official and arms-industry lobbyist, revealed that a small group of senior State Department officials had been “determined to ignore legitimate humanitarian concerns among their ranks and on Capitol Hill” to push through the arms sales last year.Mr. Pompeo has dismissed accusations at the center of the inquiry into his potential abuse of government resources and taxpayer funds, which include a possible misuse of a political appointee’s time to perform personal and political tasks for him and his wife. A congressional aide said that inquiry involved accusations that the Pompeos had asked the State Department employee to pick up dry cleaning, make restaurant reservations and walk the family dog, Sherman. People familiar with the inquiry said Ms. Porter, whose title is senior adviser to the secretary, was the political appointee.Ms. Porter has a wide-ranging portfolio at the agency. She completes tasks for Ms. Pompeo, who is a volunteer, and helps arrange domestic travel for the Pompeos — which has involved secretive meetings with Republican donors and political figures. Ms. Porter also helped Ms. Pompeo organize about two dozen lavish “Madison Dinners,” in which business executives, donors and politicians, most of them Republicans or conservatives, were invited to dine in the State Department at taxpayer expense.