The fastest man in history was reported in The Times to have labelled the Games "a bit sh*t", when speaking on Tuesday, and to have said he was "not really" having fun in Scotland.
"The Olympics were better," Bolt was quoted as saying.
The six-time Olympic champion denied making the comments, responding on his Twitter feed by saying: "I'm waking up to this nonsense..journalist please don't create lies to make headlines."
The Times reporter behind the story, Katie Gibbons, stated on Twitter that the "full conversation" with Bolt would feature in Thursday's newspaper.
As the Bolt storm engulfed the Games, with denials and statements of defence swirling behind the scenes, Bolt might have been expected to go to ground in the hope it would blow over.
Yet the 27-year-old instead headed to the women's netball match between Jamaica and New Zealand at the Scottish Exhibition and Conference Centre, having previously promised to watch the Reggae Girlz in action.
Taking up a regular seat towards the back of the VIP section, the crowd did not appear immediately aware of his presence as he sat quietly chewing gum and clapping his team.
As Bolt made his way out of the netball hall, with media shouting questions at him regarding his opinion of the Games, he shouted "awesome" in response before security ensured a swift exit.
Bolt also trained on the warm-up track at Hampden Park this afternoon, putting in some practice ahead of Friday night's 4x100 metres relay heats.
Commonwealth Games chiefs gave Bolt a VIP welcome to Glasgow on Saturday. For an athlete who will run only in the sprint relay to have a packed-out press conference all to himself must rank as a first.
Such is the nature of Bolt's status in world sport, though, and his position as easily the highest-profile competitor in Glasgow, organisers will have hoped he would shine a radiant light on the Games, rather than trigger any trouble.
For Bolt to make such disparaging comments as were attributed to him could have been a crushing blow to the Games, even causing long-term damage to the brand.
But Mike Hooper, chief executive of the Commonwealth Games Federation, said he accepted Bolt's version of events.
Hooper said: "We take Mr Bolt at his word. We're very pleased with how he's responded and that's our position."
Speaking at the daily media briefing, Hooper stressed the Commonwealth Games had its own identity and aims, different to the Olympic Games, and said he was "proud" of its status in the sporting world.
He said: "We're not trying to be the Olympic Games. We're about the celebration of the Commonwealth, sport and culture within the Commonwealth, and what a fantastic event we are seeing here in Glasgow.
"These Games continue to go from strength to strength."
He stressed the Games would "evolve positively in Gold Coast in 2018" and added: "We are who we are and proud of it."
Bolt's manager Ricky Simms told BBC Sport the remarks attributed to the athlete were "utter rubbish".
Simms added: "The atmosphere in and around the stadiums has been absolutely fantastic and I have absolutely no idea where these quotes have come from."
Bolt has been staying in the Games athletes' village as he prepares to race for the first time in 2014, after taking time to recover from a foot injury.
This is his first Commonwealth Games and since Saturday he has looked to keep a low profile, although he met the Duke and Duchess of Cambridge and Prince Harry on Tuesday.
Jamaica sprint team-mate Jason Livermore was asked on Wednesday if Bolt was enjoying Glasgow, and said: "I hope so, better than me."
Shona Robison, the Scottish Government cabinet secretary for the Commonwealth Games and sport, welcomed Bolt's clarification and expressed her delight at the success of Glasgow 2014.
Robison said: "Usain Bolt has described the comments in the media today as nonsense and dismissed them outright. 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 speaks volumes to what the real story is about these Games and about Glasgow and Scotland."