Britain's Sunday Times newspaper reported that the 24-year-old had contacted International Automobile Federation (FIA) president Max Mosley to "express his frustration" at being "misled" by the team.
It said the Briton had suggested he was so disenchanted with events that he was considering leaving the Mercedes-powered team and the sport, with the world motor sport head then advising him not to.
Hamilton had earlier been stripped of the third place awarded to him at the Australian season-opener last week after a stewards enquiry that demoted Toyota's [ Images ] Italian Jarno Trulli [ Images ] from the podium to 12th.
Hamilton apologised for his conduct at a news conference on Friday and said he had done what now-suspended McLaren sporting director Dave Ryan had told him to do.
McLaren team boss Martin Whitmarsh said he had spoken to Mosley and Hamilton's father Anthony and was satisfied the newspaper report was incorrect.
"The first I knew of it was this morning," he told reporters at the Sepang circuit. "We have asked Anthony only five minutes ago if this is true and Anthony has told us that Lewis has not spoken to Max."
"On Friday morning both I and Anthony spoke to Max ... but I am told that Lewis has not."
Asked how he saw Hamilton's future at a team that has supported him since boyhood and whether there had been discussions, Whitmarsh said: "I have read some stories this morning but I have obviously spoken to Lewis and Anthony on quite a few occasions.
"In all of those conversations, the commitment from Lewis and Anthony to this team has not altered. There has been no hint of what is reported," he said.
"At the moment, I don't believe what has been reported. What we do know is that we've got to learn from the mistakes that have been made, I've got to learn. I have made mistakes," said Whitmarsh.
"Everything that Lewis and Anthony have said to me has been incredibly appreciative and supportive of what this team has done for them and there's been no hint of anything that would cause me to believe that they would contemplate for this or any other reason leaving this team."