He tweeted that the inquiry was unfair - and reiterated there had been 'no collusion' between his election campaign and Russia.
He added that it was dominated by 'hardened Democrats' and supporters of his defeated opponent Hillary Clinton.
Mr Mueller, a highly regarded former head of the FBI, is a Republican.
The president's comments came a day after his lawyer, John Dowd, said it was time for the special counsel's investigation to end. Initially Mr Dowd said he was speaking for the president but later clarified he was 'speaking for myself'.
Donald Trump's latest tweet drew warnings from fellow Republicans about interfering with the Mueller investigation.
Why does the Mueller team have 13 hardened Democrats, some big Crooked Hillary supporters, and Zero Republicans? Another Dem recently added...does anyone think this is fair? And yet, there is NO COLLUSION!— Donald J. Trump (@realDonaldTrump) 18 Mart 2018
In earlier tweets, the president also berated former FBI deputy director Andrew McCabe, who was fired by Attorney General Jeff Sessions on Friday just two days before he was due to retire, and former FBI director James Comey, whom Mr Trump sacked last year. The latter firing led to the Mueller investigation being set up.
Mr Trump accused Mr Comey of lying under oath before Congress, and described the contemporaneous notes that Mr McCabe and Mr Comey took following discussions with him as 'fake memos'.
Mr McCabe has given memos about conversations he had with President Trump to the Mueller inquiry, US media say.
The memos could support claims that Mr Trump sought to obstruct justice.
Mr Mueller has so far indicted 19 people.
But Republican Senator Lindsey Graham said Mr Mueller should be allowed to proceed without interference, and that many Republicans shared his view.
He also warned Mr Trump against any attempt to dismiss Mr Mueller.
'If he tried to do that, that would be the beginning of the end of his presidency, because we're a rule of law nation,' Mr Graham said.
Why was McCabe fired?
Mr McCabe had been under internal investigation by the FBI and had already stepped down from his deputy post in January pending the review.
He was sacked just two days short of his 50th birthday on Sunday, when he was expected to retire with a federal pension.
Attorney General Jeff Sessions said the 'extensive and fair investigation' had concluded that Mr McCabe 'made an unauthorised disclosure to the news media and lacked candour - including under oath - on multiple occasions'.
Although the decision to fire Mr McCabe was made by Mr Sessions, Mr Trump had criticised him for months.
He has publicly pointed to donations that Mr McCabe's wife, a Democrat, received from a Clinton ally when she ran unsuccessfully for the state Senate in 2015 as evidence that Mr McCabe was politically biased.
He welcomed the news of his dismissal almost immediately after Mr Sessions announced it, calling the move a 'great day for democracy'.
What could the memos say?
News that Mr McCabe had kept records of his conversations with Mr Trump at the time he was acting FBI director emerged on Saturday.
US media say the memos will support Mr Comey's account of the circumstances of his dismissal last May.
In a statement responding to his firing on Friday, Mr McCabe vehemently denied wrongdoing.
'I am being singled out and treated this way because of the role I played, the actions I took, and the events I witnessed in the aftermath of the firing of James Comey,' his response said.
The statement alleges that the justice department report recommending his firing was 'accelerated' after he indicated that he would corroborate Mr Comey's version of events.
On Saturday Mr Comey - who is due to release a book - said Americans would soon be able to judge for themselves 'who is honourable or not'.
The Mueller probe should never have been started in that there was no collusion and there was no crime. It was based on fraudulent activities and a Fake Dossier paid for by Crooked Hillary and the DNC, and improperly used in FISA COURT for surveillance of my campaign. WITCH HUNT!— Donald J. Trump (@realDonaldTrump) 18 Mart 2018