Shanahan "has decided not to go forward with his confirmation process so that he can devote more time to his family," Trump tweeted after Shanahan faced questions over his past personal life and an allegation of domestic violence.

Trump said the army secretary, Mark Esper, will come in as acting secretary of defense.

There hasn't been a full secretary of defense since the resignation of James Mattis in December last year after splits in the administration over Trump's sudden decision to remove US troops from Syria.

The new upheaval in what is one of the biggest posts in the US government comes amid rising tensions in the Middle East, where the United States has accused Iran of attacking oil tankers in the strategic Gulf of Oman.

The Pentagon has announced another 1,000 troops are to be sent to the region, while US officials say they would launch a war if necessary to stop Iran from pursuing nuclear weapons -- something Tehran insists it is not doing.

Shanahan's nomination has been bogged down in the congressional confirmation process. The last straw appears to have been revelations during an FBI background check of a violent altercation with his then wife in 2010.

In a statement late Monday, Shanahan said it was "painful" to see his past "dredged up and painted in an incomplete and therefore misleading way as a result of this nomination process."

"I never laid a hand on my then-wife and cooperated fully in a thorough law enforcement investigation that resulted in her being charged with assault against me -- charges which I had dropped in the interest of my family," he said, according to USA Today.

Esper is a former army officer who served in the US-led 1990-1991 Gulf war to end Iraq's invasion of Kuwait, then became a senior executive at weapons and aerospace company Raytheon. Shanahan had a long career at Boeing's civil and military divisions before joining the Pentagon.