• The transition team for President-elect Donald Trump reached an agreement with the Department of Justice that sets the stage for the DOJ to conduct background checks and start the security clearance process for Trump administration nominees.
• The agreement comes amid controversy over a number of Trump's picks for top positions in the government.
• Trump intends to nominate former Fox News host Pete Hegseth as Pentagon chief, Robert F. Kennedy Jr. as secretary of Health and Human Services, Kash Patel as FBI director, and Tulsi Gabbard as director of national intelligence.

President-elect Donald Trump's transition team said Tuesday that it reached an agreement with the Department of Justice that sets the stage for the department to conduct background checks and start the security clearance process for Trump administration nominees and appointees.

The agreement comes amid controversy over some of Trump's picks for top positions in the government, including the leadership of the Defense Department, the Department of Health and Human Services, the FBI, and the post of director of national intelligence.

An agreement to have the FBI, which is a division of the DOJ, conduct background checks on nominees and appointees could make some U.S. senators more comfortable voting to approve Trump's selections for such posts than they would be without such a deal.

Susie Wiles, the incoming White House chief of staff, in a statement, said, "The agreement with the Department of Justice will ensure President Trump and his team are ready on Day 1 to begin enacting the America First Agenda that an overwhelming majority of our nation supported on Election Day."

The Trump transition team said its memorandum of understanding with the DOJ "allows the transition team to submit names for background checks and security clearances."

"Ultimately, this will afford the transition process additional insights, and it facilitates our agency landing teams gaining access to the information they need to prepare for leadership of the federal agencies and departments," the transition team said in a statement. 

The MOU was announced a day after an article in The New Yorker detailed allegations of alcohol abuse, sexual impropriety and mismanagement of two non-profit veterans groups by Pete Hegseth, who Trump has tapped to become the next Defense secretary.

Shortly after Trump announced his planned nomination of Hegseth, news broke that the former Fox News anchor had been investigated by police, but not criminally charged, for an alleged sexual assault of a woman at a Republican event in California in 2017. Hegseth has denied any wrongdoing.

Trump initial pick for U.S. attorney general, Matt Gaetz, dropped out of contention on Nov. 21 after renewed focus on allegations the former Florida congressman had sex with a girl when she was just 17 years in 2017. Gaetz also denies any wrongdoing.

Over the weekend, Trump said he would appoint his long-time loyalist Kash Patel as director of the FBI.

Patel last year vowed to target judges, lawyers and journalists who he believed were politically motivated in investigating Trump.

"Whether it's criminally or civilly, we're going to figure that out — but yeah, we're putting you all on notice," Patel told former Trump White House aide Steve Bannon in an interview. "We're actually going to use the Constitution to prosecute them for crimes they said we have always been guilty of but never have."

Trump's selection of former Hawaii congresswoman Tulsi Gabbard as director of national intelligence is another controversial pick.

"There's no question I consider her someone who is likely a Russian asset," Rep. Debbie Wasserman Shultz, D-Fla., told MSNBC, referring to Gabbard, who would oversee 18 U.S. intelligence agencies as DNI if confirmed by the Senate.

The vaccine skeptic and conspiracy promoter Robert F. Kennedy Jr., who Trump has picked to become secretary of HHS, was a heroin user for years as a teen and young adult.

Democratic senators have been especially insistent that background checks are needed for all of Trump's nominees before they can be considered for confirmation by the Senate.

Speaking Tuesday to NBC News, Democratic Sen. John Fetterman of Pennsylvania said Hegseth's nomination was part of an "ongoing dialog" among senators about Trump nominees.

"It's really appropriate, though, to have FBI background checks" to help illuminate the allegations against Hegseth, Fetterman said.

"My God, you know if you're going to be in charge of the most lethal organization in the history of humanity ... it would be entirely appropriate too to have a complete background FBI for all of that," the senator said.

The incoming Republican chair of the Senate Armed Services Committee, which would conduct Hegseth's confirmation hearing, said Tuesday that some members of his party have concerns about Hegseth.

"There are questions that some members have, and we're going to be looking for an answer," Sen. Roger Wicker, R-Miss., told NBC News.

- Additional reporting by CNBC's Christina Wilkie