Government plans to transfer anti-obesity efforts from Sport England to the Department of Health (DoH) have forced Derek Mapp, the head of Sport England, to resign.
The quango is in charge of grassroots sport and has been involved with government efforts to increase activity levels.
However, culture secretary James Purnell decided the DoH should take more responsibility for engaging people in sport, sparking a rift with Mr Mapp.
Mr Mapp resisted the changes but denies he was entirely opposed.
He voiced concerns Mr Purnell's decision to shift funding from promoting jogging and walking to traditional sports would leave Sport England under-funded.
In a statement Mr Mapp said: "I was asked to resign at a meeting with James Purnell. He said he was keen to introduce a change of direction and he said it appeared I was not very keen on the new agenda."
The former chair said he had been "dumped on" when Mr Purnell's agenda changed.
Mr Mapp added: "I accept that the DoH should be getting people fitter but their contribution over recent years has been very little."
The culture secretary has now appointed Richard Lewis, the former executive chairman of the Rugby Football League, to conduct a full review of Sport England's funding regime.
Opposition politicians have voiced alarm at Mr Mapp's resignation, questioning the government's ability to tackle rising obesity levels.
Tom Brake, Liberal Democrat Olympic spokesman, said: "At the very time when the health of the nation is threatened by an obesity epidemic, the government has dropped the physical activity baton between the sport and health departments."
With no successor to Mr Mapp yet identified, Mr Brake called on ministers to set out how the DoH plans to pick up his responsibilities.
The Conservatives welcomed the shift in responsibility, having long called for Sport England to focus on sport itself.
But shadow culture spokesman Jeremy Hunt criticised the government's wider sports policy in the lead up to the London Olympics.
Mr Hunt said: "After a decade of slashing lottery funding for grassroots sport, government policy is still failing to get a grip in the run up to 2012."