The announcement yesterday was the first public confirmation of an investigation which began last summer, and it comes at the outset of Mr Comey’s opening statement to a congressional hearing examining Russian meddling and possible connections between Moscow and Mr Trump’s campaign.
The director acknowledged that the FBI does not ordinarily discuss ongoing investigations, but said he has been authorised to do so given the extreme public interest in this case.
He told the House intelligence committee: “This work is very complex, and there is no way for me to give you a timetable for when it will be done.”
Under questioning from the committee’s top Democrat, Adam Schiff, he also publicly contradicted a series of tweets from Mr Trump which declared the Republican candidate’s phones had been ordered tapped by then-president Barack Obama during the campaign.
Mr Comey said: “I have no confirmation that supports those tweets, and we have looked carefully inside the FBI.”
The same was true, he added, of the US justice department.
He also disputed allegations that British intelligence services were involved in the wiretapping.
Mr Comey was the latest US government official to reject Mr Trump’s claims, made without any evidence, that Mr Obama had wiretapped his New York skyscraper during the campaign.
Devin Nunes, a California Republican and chairman of the House intelligence committee, also rejected the assertion earlier in the hearing.
Mr Comey was testifying along with National Security Agency director Michael Rogers.
Mr Trump took to Twitter before the hearing began, accusing Democrats of making up allegations about his campaign associates’ contact with Russia during the election.
He said Congress and the FBI should be going after media leaks – and maybe even Hillary Clinton – instead.
“The real story that Congress, the FBI and others should be looking into is the leaking of Classified information. Must find leaker now!” Mr Trump tweeted early yesterday as news coverage on the Russia allegations dominated news bulletins.
Mr Trump also suggested that Mrs Clinton’s campaign was in contact with Russia and had possibly thwarted a federal investigation.
US intelligence officials have not publicly raised the possibility of contacts between the Clintons and Moscow.
Officials investigating the matter have said they believe Moscow had hacked into Democrats’ computers in a bid to help Mr Trump’s election bid.