Details released under the Freedom of Information Act disclose that the aircraft stayed on the ground for five minutes before leaving.
According to its flight log, the helicopter - said to have been hired by Thames Valley Police - landed at Harrowdown Hill in Oxfordshire at 10.55am on 18 July 2003, 90 minutes after Kelly's body was found by search teams.
The purpose of the flight and who was on board have not been established because details of the flight log have been heavily redacted.
Dr Andrew Watt, who has raised doubts about the circumstances around Kelly's death, said: "If the purpose of the helicopter flight was innocent, one has to ask why it was kept secret."
Thames Valley Police declined to comment yesterday on whether the force had hired the aircraft or the reasons behind doing so and why the flight log had apparently been redacted.
A police spokesman said: "We have given, as a police force, all the evidence to the Hutton Inquiry. This was a full inquiry and there is nothing more to say."
Campaigners have been pressing for a full inquest to be held amid claims that the inquiry into Kelly's death failed to examine a number of questions surrounding the discovery of his body.
Kelly's death came soon after he was named as the source of BBC reports questioning the accuracy of a government dossier arguing the case for war in Iraq. The Hutton Inquiry found the government weapons inspector committed suicide in woods near his Oxfordshire home but a group of doctors denounced the report as a "whitewash" which "failed adequately to address the cause of death itself and the manner of death".