The Jamaican runner, who competes in the 4x100 relay heats at Hampden Park tomorrow, described the reports as "nonsense" while the newspaper that made the claim said it was standing by the story.
The Bolt row emerged yesterday and comes amid allegations other members of the Caribbean island team were less than enamoured with their stay. They are in contrast to those who believe the Glasgow Games have captured the imagination.
London-based newspaper The Times quoted the Olympic 100m champion as saying he was "not really" having fun in Glasgow.
But Bolt said on Twitter, the social networking site: "I'm waking up to this nonsense ... journalist please don't create lies to make headlines".
The runner's involvement in the relay is Bolt's only event at Glasgow 2014. He later told reporters he thought the Games were "awesome", but the newspaper said it was standing by its story and it remained unchanged yesterday on its website.
Bolt's representatives were not discussing whether the runner would be seeking a retraction, or whether legal action over damage to his reputation was being considered.
Bolt has spent most of his time in Glasgow in his room in the Athletes' Village.
Five-time Olympic gold medallist rower Sir Steve Redgrave entered the debate, saying he did not know if Bolt had made the comments but that the Olympics would be the platform a "world megastar" like the Jamaican sprinter would be looking for.
Sir Steve said: "I don't think the Commonwealth Games has captured his imagination or he would have been trying to compete in all the events he normally competes in, instead of just the relay, so that is a little bit disappointing.
"I think the top stars, if they are fit enough and well enough and they get the opportunity, they should be competing. I competed at one Commonwealth Games and would have loved another opportunity to have been able to do it.
"In some ways athletes always see themselves as a little bit top of the tree and more flamboyant in terms of what they say."
After 2012 London Olympics mastermind Sebastian Coe described the Glasgow Games as "raising the bar" of quality, Australian chef de mission and former Commonwealth marathon champion Steve Moneghetti dismissed Bolt's alleged comments.
"One person's views differ from people in here. The masses here say it's been an outstanding Games to this point," said Moneghetti.
"Our athletes have found these Games exceptional - they have had a great experience. They have lived in the village, every one of them.
"So we are a team here. The training and competition venues are great and the volunteers and people of Scotland have looked after us fantastically."
Bolt, who has not raced all season, withdrew in June from the 100m and 200m sprints in Glasgow, saying he was returning to full speed from a foot injury.
His Jamaican training partner Yohan Blake also withdrew after suffering a hamstring injury that requires surgery in the 100m at the Glasgow Grand Prix in July.
On social media yesterday he said: "Atmosphere looks fantastic. Track looks fast. Kudos to organisers. Wish I was there."
Meanwhile, another Jamaican sprinter, Jason Livermore, also expressed disquiet about the Games.
Asked what he was making of the life in the Athletes' Village and his well-being he said: "Well, it can be better - things can be a little bit better for us. Can be better in a lot of sense.
"We have to just enjoy and give God thanks."
Speaking after his 200m heat, he added: "I hope Usain's having a better time than me. The people in Scotland are very welcoming so I can't complain. There's a nice atmosphere and a nice crowd.
"But it's very cold. Back in Jamaica it is not like this. I need to get me some clothes. It is freezing."