Speaking at a rally in Springfield on Friday night, the US president told his supporters there were “real bad ones” in the government bodies.
“Look at what’s now being exposed in our Department of Justice and the FBI,” he said. “We have great people at the Department of Justice … but you have some real bad ones. You’ve seen what happened at the FBI – they’re all gone.
“But there’s a lingering stench and we’re going to get rid of that too,” Mr Trump added.
Mr Trump’s comments came just hours after news broke that deputy attorney general Rod Rosenstein had reportedly considered secretly recording his conversations with the president and had also discussed ways the 25th Amendment could be used to oust him from office.
First reported in The New York Times on Friday, Mr Rosenstein denied the allegations as “absolutely false”.
Mr Trump did not mention Mr Rosenstein by name during his latest speech, but has repeatedly attacked the Justice Department’s leadership and the decision to appoint special counsel Robert Mueller.
Some conservative commentators called for the president to fire Mr Rosenstein following the claims in The New York Times.
The president did use the rally in Missouri – held for the Republican Senate candidate Josh Hawley – to champion his Supreme Court pick Brett Kavanaugh.
Mr Kavanaugh is facing an allegation he sexually assaulted Christine Blasey Ford when they were both in high school more than 30 years ago.
Mr Trump described the nominee as a “fantastic man” and urged his supporters “to fight for him, not worry about the other side”.
“Women are for him more than anyone would understand,” said the president.
He had earlier tweeted that the assault could not have been “as bad as she says,” or she would have reported it sooner.
The Springfield crowd were heard chanting Mr Kavanaugh’s name.
The chairman of the Senate Judiciary Committee has agreed to give Ms Ford more time to decide whether to testify before the committee and publicly detail her claims next Wednesday.
Ms Ford’s attorney Debra Katz said her client had yet to decide whether to speak and described an initial Friday night deadline imposed by the committee as “arbitrary”.
Senator Chuck Grassley explained in a tweet late Friday that he had granted Ms Ford’s lawyers’ request for an extension.