The complaint comes from Patrick Cox, chief executive of the Male Cancer Awareness Campaign, who believes the 'gold bond' scheme could be considered a cartel for charities with household names. Bond holders get five places for runners for five years, and can renew them if they want to.
"We are asking the OFT to investigate because we believe the selection and distribution of gold bond places is outdated and unfair," said Cox.
"We have taken legal advice and believe the marathon may be in breach of UK and EU competition law."
Cox said he was moved to act by the "endless frustration" of people who wanted to run for his charity in the marathon but were faced by a five-year waiting list.
The Office of Fair Trading said it was undertaking an "information-gathering process" before deciding whether to launch a formal investigation.
Cox claimed that the gold bond system was a "golden handshake" that was nearly always renewed every five years and enabled the largest charities to obtain the most income.
"To me there is a strong smell about the gold bond system, and it is the sickly, nasty smell of greed," said Cox. "That is something that should not be in the charity sector."
He called for a new system in which places were rotated every year. "This would allow charity causes to be represented by different charities each year and would reduce saturation by the main charities," he said.
A silver bond scheme was introduced last year after a campaign by a coalition of charities led by the Royal Blind Society (Third Sector, 16 November 2005).
The scheme, which starts in 2007, will offer one place every five years to up to 1,250 charities.
The London Marathon was unavailable for comment.