President Donald Trump's pick to run the Pentagon has taken himself out of the running following media reports that near decade-old domestic disputes were holding up his FBI background checks.

Patrick Shanahan, the former Boeing executive Trump planned to nominate to replace Jim Mattis as defense secretary, "decided not to go forward with his confirmation process so that he can devote more time to his family," Trump tweeted on Tuesday.

The announcement follows a report from USA Today that the FBI was looking into a violent domestic dispute between Shanahan and his former wife during which both claimed they'd been punched by the other. While Shanahan said he "never laid a hand" on then-wife Kimberly Jordinson, according to the paper, she said she stands by her account.

In 2011, Shanahan also came to the defense of his son, who beat his mom -- Shanahan's ex-wife -- with a baseball bat. The incident left her "unconscious in a pool of blood, her skull fractured and with internal injuries that required surgery," the Washington Post reported.

At the time, Shanahan wrote in a memo to Jodinson's brother that his son had acted in self-defense, the Post reported. But, he told the paper, he doesn't believe violence is appropriate ever, and would never justify someone attacking another person with a baseball bat.

Shanahan was likely to face questions from lawmakers about the incidents, which were reportedly holding up his FBI background checks, during his Senate confirmation hearing. Having the family disputes aired publicly "will ruin my son's life," Shanahan told the paper.

The confirmation process should focus on national security, readiness and the future of the military, Shanahan said in a statement. Instead, Shanahan, who was confirmed to serve as deputy defense secretary more than two years ago, said a "deeply personal family situation from long ago is being dredged up and painted in an incomplete and therefore misleading way."

"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," Shanahan said. "Ultimately, their safety and well-being is my highest priority.

"I would welcome the opportunity to be Secretary of Defense," he added, "but not at the expense of being a good father."

The family disputes weren't the only controversy Shanahan has faced since becoming the longest-ever acting defense secretary earlier this year when Mattis stepped down in protest of Trump's policies. The Pentagon inspector general's office investigated claims that he used his position to promote Boeing, his former employer.

Related content:

Ultimately, investigators found he "fully complied with his ethics agreements and his ethical obligations regarding Boeing and its competitors."

Army Secretary Mark Esper will step into the acting defense secretary role, Trump tweeted. Esper, a Harvard grad and retired Army infantry officer who served during the Gulf War, has been Army secretary since 2017.

Esper is also the former vice president of government relations at Raytheon, a defense contractor.

"I thank Pat for his outstanding service and will be naming Secretary of the Army, Mark Esper, to be the new Acting Secretary of Defense," the president wrote. "I know Mark, and have no doubt he will do a fantastic job!"

Army officials said they had no immediate comment on the announcement. At least one watchdog group is already speaking out about Esper being tapped to lead the Pentagon, even if temporarily.

"I'm not thrilled that the next acting defense secretary is a former Raytheon executive," Mandy Smithberger, director of the Project On Government Oversight's center for defense information, said in a statement. "As tensions increase over Iran, we need a permanent Secretary of Defense who has the credibility necessary to make sure the Pentagon is acting in the best interests of our national security, not what's in the best interest of contractors."

Esper has pushed the Army to consider redesigning its formations for fighting on more complex battlefields and says the service needs modern weapons systems so the U.S. military can keep its edge over the enemy.

As Shanahan steps down, he said he would coordinate an appropriate transition plan to ensure troops receive the support they need. He called leading them a deep honor and privilege.

"I am proud of the work accomplished over the last two years," he said. "With the leadership of President Trump and the bipartisan support of Congress, the Department has made significant progress rebuilding and modernizing the military to compete with China and Russia."

Shanahan, who oversaw the development of the Space Force and other cyber and weapons' program advancements during his time as acting and deputy defense secretary, said the Pentagon is postured for long-term security.

"I have the greatest confidence in our civilian and military leaders and the vitality of the institution," he said.

-- Matthew Cox contributed to this report.

-- Gina Harkins can be reached at gina.harkins@military.com. Follow her on Twitter @ginaaharkins.