LMCs warned the move will free practices to ditch innovative schemes that are working well.
Official figures show a drop in practices offering extended hours in the region as certain local enhanced agreements (LES) are no longer being counted towards PCT targets.
A DoH spokeswoman said that exceptions could be made for some local agreements but others would have to be 'adjusted' to meet national criteria.
A spokesman for NHS North West, the region's SHA, said practices in Heywood, Middleton and Rochdale PCT were targeted particularly, but other LES deals were also deemed unacceptable.
'There has been a clarification of how the DoH classifies practices offering extended hours. Certain practices no longer count towards extended hours targets,' said the spokesman.
A spokesman for Heywood, Middleton and Rochdale PCT said its LES would have to be changed. Innovative schemes, where GPs run extended hours clinics in a supermarket, would have to take place within a GP practice instead, he said.
LMCs across England said last month that the DoH is pressuring SHAs and PCTs to scrap flexibilities in LESs that allow concurrent working.
GPC negotiator Dr Chaand Nagpaul said the government's 'control freakery' was inexplicable. 'This makes a mockery of the concept of a LES being negotiated locally. It baffles me why the government should spend its time interfering with local decision making.' He said it would be damaging for practices that have signed up to an agreement that will have to change.
A GP investigation found up to 97 per cent of PCTs had developed a LES to fund practices opening extended hours (GP, 8 August).
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