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Mr Trump accused US spies of leaking allegations that Russia had compromising material on him.
But James Clapper, director of National Intelligence, said he was "profoundly dismayed" by the leak.
He also said the intelligence community had not "made any judgment" that the information was reliable.
His statement said he had spoken to Mr Trump on Wednesday evening.
"I emphasised that this document is not a US Intelligence Community product and that I do not believe the leaks came from within the IC."
Mr Clapper said they agreed the security breach was "extremely corrosive and damaging to our national security" and the intelligence community "stands ready to serve his administration".
The president-elect gave a press conference in which he responded to unsubstantiated allegations that his election team colluded with Russia and there were salacious videos of his private life.
CNN first reported the claims on Tuesday, although did not give details, and then Buzzfeed published a 35-page dossier of allegations.
An enraged Mr Trump pointed the finger and said: "I think it's pretty sad when intelligence reports get leaked out to the press."
He called Buzzfeed a "failing pile of garbage" and refused to take a question from a CNN reporter.
Tensions between Mr Trump and the intelligence agencies have been strained in recent weeks.
The president-elect had failed to accept assessments that Russia had hacked the Democratic Party to help Mr Trump win the election.
On Tuesday, FBI Director James Comey refused to say whether the FBI was investigating any possible ties between Russia and Trump's presidential campaign.
Christopher Steele is understood to be the author of the series of memos regarding Donald Trump which have aroused such controversy.
Mr Steele is said to be a former member of the British Secret Intelligence Service MI6 and a director of Orbis - which describes itself as a leading corporate intelligence company.
The research is believed to have been commissioned initially by Republicans opposed to Mr Trump and consists of extensive allegations about his personal life, business deals and his campaign's relationship with the Russian state. However, the allegations have not been independently substantiated or verified and some details have been challenged as incorrect by those who are mentioned.
Mr Trump himself was briefed about the existence of the allegations by the US intelligence community last week but has described them as "fake news".
Mr Steele did not respond to a request for comment.
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