The UK's biggest fundraising event has traditionally had two official charity partners, one selected by the race organisers, the other by event sponsor Flora.
Each partner receives 250 golden bonds. Under the new arrangements, however, only one charity will benefit and the surplus bonds will go to other organisations. Each bond gives a charity five places for runners.
Speaking at an Institute of Fundraising conference in London last week, David Bedford, race director of the marathon, said more charities would benefit.
"The spare places will go back into the golden bonds scheme," he said. "There are 400 charities on the waiting list; it will allow us to offer bonds to 50 of those."
More than 600 charities currently share 2,750 golden bonds, but the race organisers do not disclose how many each organisation has.
"There is not an infinite number of places in the marathon," said Bedford. "Every group says the bond system is not fair, but we're as reasonable as it's possible to be."
The decision means the Spinal Injuries Association and Heart UK will next year be the last organisations to be joint charity partners with the marathon.