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".--BBC