The bombshell was an unusual move given the FBI does not usually comment on ongoing investigations.
“But in unusual circumstances, where it is in the public interest,” Mr Comey said, “it may be appropriate to do so.”
Mr Comey also dismissed the president's claims that Barack Obama ordered the wiretapping of Trump Tower.
Image Caption:Donald Trump has said he would release information on the alleged wiretapping
Both he and NSA director Admiral Mike Rogers emphatically rejected claims GCHQ carried out surveillance on behalf of the Obama administration.
They said that such an order would be a violation of US law and Mr Trump's accusation “frustrates the relationship with a key ally”.
Mr Comey referred directly to President Trump's tweets about the surveillance on Trump Tower when he said: “With respect to the president's tweets about alleged wiretapping directed at him by the prior administration, I have no information that supports those tweets, and we have looked carefully inside the FBI.”
Video:FBI director James Comey tells a Congressional hearing that his agency and the Department of Justice has no information that support tweets made by Donald Trump that GCHQ bugged Trump Tower.
Both men were speaking at the first Congressional intelligence committee public hearing on alleged Russian interference in the 2016 election.
For months it has been the consensus of the US intelligence community that Russia used a portfolio of propaganda including hacking and 'fake news' to hurt Hillary Clinton's campaign and help Mr Trump.
White House officials said “nothing has changed” after it emerged that the FBI was investigating links between the Kremlin and the president.
“There is NO EVIDENCE of Trump-Russia collusion and there is NO EVIDENCE of a Trump-Russia scandal,” a senior administration official said in a written statement.
Video:Spicer: You can look for something that doesn't exist
FBI director James Comey and NSA director admiral Mike Rogers said during their testimony that Russia did not hack ballot counts, but did try to influence the election in Mr Trump's favour.
The Congressional panel's top Democrat said before the hearing got under way that material it received from the FBI showed there was circumstantial evidence American citizens colluded with Russians during the election campaign.
White House press spokesman Sean Spicer, when asked later about alleged Russian collusion, said there had been no evidence presented.
With respect to other matters discussed at the hearings, he said there was much that had yet to come out.
Mr Trump took to Twitter before the hearing began, accusing Democrats of making up allegations about his campaign and saying the FBI should be going after media leaks.