The Times reporter, Katie Gibbons, claims Bolt told her that he thought "the Olympics were better", that he was "not really" having fun in Glasgow and felt the Games were "a bit shit", reports CMC.
However the 27-year-old sprinter has dismissed reports of his comments as "nonsense".
"I'm waking up to this nonsense," Bolt tweeted.
I'm waking up to this nonsense..journalist please don't create lies to make headlines— Usain St. Leo Bolt (@usainbolt) July 30, 2014
"Journalist please don't create lies to make headlines".
However, the Times' Scottish editor, Angus Macleod, says he had full confidence in Gibbons.
"We stand by this story 100 percent," he said.
"We have utter confidence in this story."
Reports here suggest that the Times were considering whether to publish a full transcript of the short interview with Bolt in Thursday's paper.
Meanwhile, Bolt's agent, Ricky Simms has also dismissed the reports as "utter rubbish".
"The atmosphere in and around the stadiums has been absolutely fantastic and I have absolutely no idea where these quotes have come from," said Bolt.
Games officials say the row is not diverting attention from the track and field action.
"We take Mr. Bolt at his word. His tweet says it all. These are fantastic Games," said Mike Hooper, the chief executive of the Commonwealth Games Federation.
"As you saw at his press conference Saturday, he is very upbeat. He is really positive about running the relay and I don't wish to comment on the journalist and work of the Times."
Bolt is competing only in the 4x100m relay after struggling with a foot injury the whole season.