In a tweet, CNN's Brian Stelter said the office had been evacuated and that CNN was airing taped programming. Bomb threat. We're running taped programming.
"The caller with a Southern accent had claimed there were five bombs placed around the building", he reported.
The bomb threat was made just 20 minutes after President Trump tweeted that fake news was "the enemy of the people" - the latest in many of his attacks on the media.
CNN's NY offices and studios have been evacuated due to a phoned bomb threat, the company says.
Alarm bells went off in the CNN newsroom after 10 pm, signaling the evacuation.
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And network host Don Lemon tweeted that the offices were evacuated in the middle of his live show, which was taken off the air.
A bomb squad was on standby outside the building as police officers search the offices, a law enforcement source said.
All vehicle and pedestrian traffic around the CNN offices had also been blocked by police, said New York Police Detective Hubert Reyes.
The threat comes less than an hour after President Donald Trump tweeted about "fake news", a phrase which he has often labelled CNN with.
"The NYPD has now given us the all clear, and employees have been permitted to return to the building".
In October, Time Warner Center was evacuated after a package containing an explosive device addressed to ex-CIA Director John Brennan was discovered.