The fastest man in the world is said to have told the Times the Games were ''a bit shit'' and he was ''not really'' having fun in Glasgow.
Jamaican Bolt, 27, sent a tweet describing the claim as "nonsense" but the newspaper said it stands by the story.
The six-time Olympic champion is said to have made the comments outside the athletes' village yesterday but said on Twitter this morning: ''I'm waking up to this nonsense..journalist please don't create lies to make headlines.''
Bolt's manager Ricky Simms, meanwhile, told BBC Sport the remarks attributed to the athlete were ''utter rubbish''.
He said: ''The atmosphere in and around the stadiums has been absolutely fantastic and I have absolutely no idea where these quotes have come from.''