Robert Hill, a consultant to Tony Blair, said there was a "severe deficit" in funding the diplomas that needed to be addressed urgently.
At present, schools are being forced to dip into their own budgets to pay for the partnerships, yet the majority of them had less than pound;100,000 funding.
Although league tables were introduced by a Conservative government, they have played a major role in New Labour's target-driven strategy to raise standards. Heads say that they dominate their lives.
John Dunford, general secretary of the Association of School and College Leaders, said there were heads of some neighbouring schools who did not even talk to each other. "The performance tables encourage direct competition between schools," he said.
This week Mr Hill said the education system was moving from 1990s-era competition to an emphasis on partnership and collaboration - but the Government still ranked schools against each other.
The schools admissions code and league tables needed to be redesigned to recognise how schools were working together, he said.
With students studying different courses at different institutions, it made no sense to rank schools on league tables. Mr Hill said heads regarded partnership as desirable but would always placed the interests of their school and pupils first.
"It is not surprising that some headteachers take the view that, since it is their head on the block if things go pear-shaped, they will only collaborate where and when it is in the direct interest of their school to do so," he said.
Partnership is way ahead, page 28.