Speculation mounted that the US leader was being probed after he claimed on Twitter that his predecessor, Barack Obama, had ordered wiretaps on Trump Tower during the presidential campaign.
Asked whether Mr Trump is being investigated, a Justice Department official told The New York Times it had “no comment”.
This would be standard practice in normal circumstances on the status of any investigation and there is not suggestion that inquiries have been launched into the President.
Mr Trump accused his predecessor of executing the wiretaps earlier this month.
“Terrible! Just found out that Obama had my ‘wires tapped’ in Trump Tower just before the victory. Nothing found. This is McCarthyism!” he tweeted.
“Is it legal for a sitting President to be “wire tapping” a race for president prior to an election? Turned down by court earlier. A NEW LOW!” he later added.
Terrible! Just found out that Obama had my "wires tapped" in Trump Tower just before the victory. Nothing found. This is McCarthyism!— Donald J. Trump (@realDonaldTrump) March 4, 2017
The President’s claims of wiretapping raised the question of whether Mr Trump might indeed be the subject of an investigation.
By accusing Mr Obama of ordering the wiretapping, the President depicted himself as the victim of surveillance, rather than an investigatory target.
No evidence was produced to support his allegations, which Mr Trump has asked the House and Senate intelligence committees to investigate.
Senior officials close to the FBI chief said he has privately asked the department to dismiss the claims as they imply that the FBI has acted illegally, The New York Times reported.
He insisted that the President is not the subject of a counterintelligence investigation concerning contacts with Russia, but he admitted that the White House does not know whether Mr Trump is being investigated.
Two senior senators leading the congressional inquiry into Russia’s alleged efforts to sway the US election have asked the FBI and Justice Department to release any information they have on Mr Trump’s claim that Mr Obama ordered the wiretapping during the election campaign.
In a letter addressed to Mr Comey and acting deputy attorney general, General Dana Boente, Republican Lindsey Graham and Democrat Sheldon Whitehouse wrote: “We request that the Department of Justice provide us copies of any warrant applications and court orders ... related to wiretaps of President Trump, the Trump campaign, or Trump Tower.”
The senators said they would take very seriously “any abuse of wiretapping authorities for political reasons”.
They added: “We would be equally alarmed to learn that a court found enough evidence of criminal activity or contact with a foreign power to legally authorise a wiretap.”
A US law professor has said Mr Trump’s unsubstantiated claims could be a “major scandal” that “could get the current President impeached,” if proven false.
“Given how great the executive’s power is, accusations by the President can’t be treated asymmetrically,” Harvard Law School professor Noah Feldman wrote in an article for Bloomberg. “If the alleged action would be impeachable if true, so must be the allegation if false.
“Anything else would give the President the power to distort democracy by calling his opponents criminals without ever having to prove it.”
Representatives for Mr Obama have vehemently denied that the former President made any kind of surveillance order on Trump Tower.
The Independent has contacted the Justice Department for comment.