The world's fastest man accused The Times newspaper of "creating lies to make headlines" after it reported he rubbished the 2014 Games while waiting for a car outside the athletes' village.
Asked he was having a good time in Glasgow, the Jamaican sprint star replied "not really" and said that the London 2012 Olympics "were better", according to The Times.
But Bolt's manager called the claims "rubbish" and the athlete himself took to Twitter to deny the report. (Also read: India's Chandrakant Mali Wins Bronze in Weightlifter)
"I'm waking up to this nonsense... journalist please don't create lies to make headlines," he wrote.
The six-time Olympic gold medallist is due to make his first appearance in the Commonwealth Games at the 4x100 metres heats on Friday, with the final on Saturday.
Organisers are already reeling from the withdrawal of top stars including double Olympic champion runner Mo Farah, cyclist Mark Cavendish and London 2012 heptathlon heroine Jessica Ennis-Hill, while Bolt will only appear in the relay event.
A Commonwealth Games Federation spokesman brushed off the reports, saying: "The Glasgow Games have so far been fantastic and everyone there, including the competing athletes, seems to be having a brilliant time."
Bolt's manager Ricky Simms earlier told the BBC that the reports were "utter rubbish". (Related: Jamaica and Kenya Dominate Commonwealth Games Track and Field Events)
"The atmosphere in and around the stadiums has been absolutely fantastic and I have absolutely no idea where these quotes have come from," he added.
Bolt arrived in Glasgow on Saturday, and endured an uncomfortable press conference in which he was asked questions about the ongoing crisis in Gaza and the Scottish independence debate.
Since then he has largely kept a low profile, but on Tuesday met Prince William, his wife Catherine and his brother Prince Harry.