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The White House shocked Washington by announcing that James Comey “has been terminated and removed from office”.
But Democrats said he was fired because the FBI was investigating alleged links between the Trump campaign and Russia.
The move came as it emerged Mr Comey gave inaccurate information to Congress last week about Mrs Clinton’s emails.
An FBI investigation into her use of a private email server to store sensitive information while secretary of state remains closed. Mr Comey said in July last year it was careless but not criminal.
The White House said the search for a successor for Mr Comey would begin immediately. In a tweet on Wednesday morning, Mr Trump said Mr Comey would be replaced “by someone who will do a far better job, bringing back the spirit and prestige of the FBI”.
It is only the second time the head of the FBI has been fired.
President Trump wrote in a letter to Mr Comey that he agreed with US Attorney General Jeff Sessions’ recommendation that “you are not able to effectively lead the Bureau”.
Mr Sessions said the department of justice was “committed to a high level of discipline, integrity, and the rule of law”, and “a fresh start is needed”.
Many have expressed surprise that Mr Comey should be fired for his handling of the investigation into Mrs Clinton’s emails, given that Mr Trump once praised the FBI director’s conduct in the matter.
In the final days of the presidential campaign, Mr Trump told a rally it “took guts” for Mr Comey to reopen the inquiry. “What he did brought back his reputation,” Mr Trump said.
But on Tuesday, Deputy Attorney General Rod Rosenstein said he “cannot defend the director’s handling of the conclusion of the investigation of Secretary [of State Hillary] Clinton’s emails, and I do not understand his refusal to accept the nearly universal judgement that he was mistaken”.
“Almost everyone agrees the director made serious mistakes; it is one of the few issues that unites people of diverse perspectives.”