The National Association of Governors and Managers has told ministers it wants a parliamentary or Audit Commission investigation into government funding of the National Governors' Council.
NAGM chairwoman Jane Phillips said the cash - in excess of pound;1 million - gives NGC an unfair advantage.
NAGM has also started accepting local authority governor associations as members: 95 are currently NGC members.
Chris Gale, NGC's chairwoman, said: "If NAGM wants to compete for our members, fine. We think more money should be put in governors' budgets so they can choose which organisation they want to represent them."
A Department for Education and Skills spokesman said: "There is room for two representative bodies for governors."