Correction & clarification: A previous version of this story misstated the title of Rep. Mac Thornberry. He is the ranking Republican on the House Armed Services Committee.

WASHINGTON – Acting Defense Secretary Pat Shanahan said Tuesday that he will resign after coming under scrutiny over a violent fight with his wife nine years ago, leaving the military top leadership in transition even as it prepares for a possible confrontation with Iran.

The announcement, disclosed in a tweet by President Donald Trump, injects uncertainty into the highest echelon of the national security system at a time of escalating tensions with Iran, which the Trump administration blamed for attacks on two oil tankers in the Gulf of Oman this month. The Pentagon ordered 1,000 U.S. troops deployed to the region Monday.

A Pentagon spokesman said in a statement that Shanahan's resignation will take effect Sunday night.

Shanahan, 56, has been the acting defense secretary since January, the longest period the Pentagon has been led by a temporary chief. Senior lawmakers from both parties said Tuesday they were concerned that the lack of a permanent defense secretary will complicate U.S. relationships with its allies and could undercut efforts to deal with security threats.

"The uncertainty surrounding this vacant office encourages our enemies and unsettles our allies," said Rep. Mac Thornberry of Texas, the top Republican on the House Armed Services Committee.

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"I am deeply concerned that the Department of Defense has no permanent leader, and that sends exactly the wrong message to the world," said Sen. Richard Blumenthal, D-Conn., a member of the Armed Services Committee. "The picture of the Department of Defense is one of turnover and turmoil at the top levels."

Trump said in April that he planned to make Shanahan his permanent defense chief, but the White House had not formally submitted his nomination to the Senate, which must vote to approve Cabinet officials.

Trump announced Shanahan's resignation about an hour after USA TODAY published a story revealing that before Shanahan's potential confirmation hearing, the FBI investigated a violent fight in 2010 between Shanahan and his then-wife. Trump said in the tweet that Shanahan was leaving to spend more time with his family.

Trump said he would replace Shanahan with Army Secretary Mark Esper, a West Point graduate, and nominate him to be the permanent defense chief.

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Two officials familiar with the matter said Trump was prepared to back his nominee, but Shanahan told the president he was pulling out in an Oval Office meeting that took place shortly after the USA TODAY story was published. Trump said he did not ask Shanahan to withdraw.

"The acting secretary met with the president and told him he didn't want to be a distraction to the Defense Department," one of the officials said. "He didn't want to be a distraction to the administration or to the president."

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'Deep honor and privilege'

In a statement, Shanahan described his time at the Pentagon as "a deep honor and privilege to serve our country alongside the men and women of the Department of Defense."

"I am proud of the work accomplished over the last two years," he said, adding that the department made "significant progress rebuilding and modernizing the military to compete with China and Russia."

He said, "I believe my continuing in the confirmation process would force my three children to relive a traumatic chapter in our family's life and reopen wounds we have worked years to heal. Ultimately, their safety and well-being is my highest priority. I would welcome the opportunity to be Secretary of Defense, but not at the expense of being a good father."

Shanahan and his former wife, Kimberley Jordinson, acknowledged in court filings and police reports that a late-night argument spilled from their bedroom to the front yard of their home in an affluent Seattle neighborhood and escalated into a clash that police said left him with a bloodied-nose and hand and her with bloodstains – possibly from offensive moves – on her forearm.

Shanahan's background:FBI examining 2010 domestic fight involving Shanahan; accounts differ on aggressor

Their accounts diverge sharply on who was to blame, as well as the claim Jordinson reported to officers that night and later outlined in divorce papers: that Shanahan punched her in the stomach. Shanahan, in a statement to USA TODAY, denied that he ever struck his wife.

Blumenthal said he was troubled that he and other senators were unaware of the allegations in Shanahan's past and that he may have failed to disclose that information to the Senate. Shanahan received Senate confirmation for the Pentagon's No. 2 job in 2017.

"I’m deeply concerned that the full truth may not have been forthcoming," Blumenthal said. "And the committee is due an explanation. I’m not alleging wrongdoing or criminality. I simply want full disclosure of who knew what and when."

Trump selected Shanahan as the Pentagon’s second-in-command in 2017, his first government posting after a career as an engineer and top executive at Boeing, a major defense contractor. The decision put Shanahan in one of the government’s top national security positions, though one where his personal life remained mostly unexamined.

Trump elevated Shanahan to be acting defense secretary after Jim Mattis resigned in December in protest of Trump’s treatment of allies and decisions to withdraw U.S. forces from the Middle East.

Questions about vetting process

Sen. Jack Reed of Rhode Island, the senior Democrat on the Armed Services Committee, knew that Shanahan had been involved in a contentious divorce when he was confirmed as deputy defense secretary but was unaware of the extent of domestic violence, his spokesman, Chip Unruh, said. He said the incident could have been overlooked in an earlier background check or might have surfaced because he was in line for the more sensitive post.

Sen. Elizabeth Warren, D-Mass., said the fight "raises serious questions about how this administration is conducting its vetting processes and needs to be investigated.”

Two FBI agents questioned Jordinson in early June about the incident in 2010 as part of a background examination of the presumptive nominee, she said. The FBI declined to comment. A Senate staffer with knowledge of the matter said the bureau’s inquiry into Shananan’s background was ongoing as part of the vetting process.

Trump said Tuesday he had been unaware of possible issues in Shanahan's background but defended his administration's handling of his nomination.

“I had heard about it yesterday for the first time," Trump said of the domestic violence incident. "I didn’t know about it. I heard about it yesterday. It’s very unfortunate, very unfortunate.”

'Trying to get on with my life'

Jordinson maintained that Shanahan struck her as the two struggled over a briefcase, an allegation she repeated to Seattle police, in a divorce filing and in an interview with USA TODAY.

“My husband is throwing punches at me,” Jordinson told a Seattle 911 operator that night, according to a recording of the call. “He’s been hitting me. … I don’t need a medic, I need you guys to get him out of the house. … He’s just swinging punches at me.”

One of the couple’s sons, who witnessed part of the argument, submitted a statement recounting a physical struggle and his mother’s call for help, though the son said he did not see either parent strike the other.

The son, Will, who was 15 at the time of the incident, asserted his mother “coerced” him to sign the document meant to assist her defense, according to a statement he provided to USA TODAY. He said the initial declaration, which indicated that police treated his mother “unfairly,” was “false, dishonest and did not represent the accurate facts.”

“I did what she told me,” he said.

Jordinson stood by her account in an interview with USA TODAY in May and said her son’s statement in 2010 was his idea. "I'm just trying to get on with my life," she said Tuesday.