The fastest man in the world is said to have told the Times the Games were ''a bit s***'' and that he was ''not really'' having fun in Scotland.
Jamaican Bolt, 27, sent a tweet dismissing the report 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.''
He appeared relaxed during a later appearance at the SECC where he cheered on Jamaica in the netball.
All camera lenses were on the star who smiled and clapped during the match which saw his side beaten by New Zealand.
Security was tight as he left the hall at around 1pm but he stopped to sign autographs and shouted "awesome" in response to reporters' questions about his enjoyment of the Games.
Bolt arrived in Glasgow at the weekend and confirmed he would be running the 4x100m relay heats on Friday ahead of the sprint relay final which takes place the following day.
It marks a Commonwealth Games debut for the sprinter who has yet to race this year after taking time to recover from a foot injury.
His decision to compete in Glasgow was a huge boost for the Games, with stars including Mo Farah, Jessica Ennis-Hill and Mark Cavendish not taking part.
The Times newspaper's Scottish editor Angus Macleod said: "We stand by this story 100%. We have utter confidence in this story."
The reporter behind the article meanwhile said on Twitter that the ''full conversation'' with Bolt would feature in Thursday's edition.
Following the athlete's dismissal of the report, Commonwealth Games Federation chief Mike Hooper said he would take Bolt at his word.
He told the daily Games briefing: "We're very pleased with how he's responded and that's our position."
Glasgow 2014 spokeswoman Jackie Brock-Doyle said: ''His tweet says it all. He has woken up to something he didn't believe he said yesterday."
Bolt's manager Ricky Simms earlier 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.''
Shona Robison, Scotland's Cabinet Secretary for the Commonwealth Games, said: "Glasgow is fantastic and the Games have been amazing on so many fronts, so well organised and a great experience for everyone involved. That is what everyone who has been here has said.
"Visitors and athletes are feeding back that they are having a great time and I think that speaks volumes to what the real story is about these Games and about Glasgow and Scotland."