The attack on 7 May, which killed three Chinese journalists and injured 20 diplomats, was condemned by China at the time as a "war crime".
Nato and the Allies have always maintained the bombing was a mistake.
But the Observer newspaper reports that the embassy, in Belgrade, was taken off a prohibited targets list after Nato intelligence detected it sending army signals to the Yugoslav forces.
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But Mr Cook said there was "no truth in this" on BBC One's Breakfast With Frost.
He said: "I know not a single shred of evidence to support this rather wild story."
"It was a tragic mistake," he said, adding that it was a "delusion" that the US had been "sitting on the information but had not shared it".
![[ image: width=150]](/olmedia/475000/images/_477374_cook150.jpg)
A Nato spokesman later said: "We are denying this story. The bombing was a mistake caused by human error, nothing else."
However, an unnamed Nato intelligence officer who monitored Yugoslav radio traffic from Macedonia told the Observer: "Nato had been hunting the radio transmitters in Belgrade.
"When the president's residence was bombed on 23 April, the signals disappeared for 24 hours.
"When they came on the air again, we discovered they came from the embassy compound."
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The report could cause diplomatic strain as the UK prepares to host an historic state visit by President Jiang Zemin of China.
The visit, which begins officially on Tuesday with a ceremonial welcome, comes amid improving relations between China and the UK since the handover of Hong Kong in 1997.
'Serious issues'
Mr Cook remained upbeat about the visit, and said "limited" progress had been made recently with China over its human rights record, following "intense dialogue".
He said there were still "serious issues" that needed to be addressed, but "we did secure the first visit to China by Mary Robinson, the UN Commissioner for Human Rights to China".
He said the real reason for the state visit was because the Queen went to China in the 1980s and President Jiang was paying a return visit.
He will be the first Communist leader to stay as a guest of the Queen at Buckingham Palace.
UK prepares Chinese charm offensive
(16 Oct 99 | UK)
China rejects US apology
(17 Jun 99 | Asia-Pacific)
Nato hits Chinese embassy
(08 May 99 | Europe)
The Observer
MOD
Nato
Chinese Ministry of Foreign Trade and Economic Co-operation
Serbian Ministry of Information
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