Members of the poorest education authorities have written to Michael Gove, warning him that the pupil premium - one of the Coalition's flagship policies - is widening the gap between the worst and best-funded schools.
The f40 Group, a campaign body lobbying for a fairer school funding system, also urged the education secretary to speed up his plans to introduce a national funding formula that, it is hoped, will reduce inequality among schools.
Currently, funding between secondary schools can vary as much as #163;1,800 per pupil and #163;1,300 per pupil in primary schools. The Department for Education is consulting on bringing in a system that aims to be fairer for all schools, and in the meantime has introduced a pupil premium, which gives additional money to schools attached to pupils receiving free schools meals.
But in a letter, members of the f40 Group cautioned Mr Gove, telling him extra funding is creating even greater differences between the best and worst-funded areas. "The pupil premium has not created the shift in allocations of funding required to fundamentally change the position of the poorest-funded authorities and schools," the letter said.
"In fact, because it adds yet more funding for deprived pupils in all authorities (including the well funded), it has further increased the differential in funding for our members."
The move to attack the scheme - which gives an extra #163;488 to the poorest pupils - came just days before it was extended to all children that have been registered for FSM in the last six years, not just those who receive them now.
The letter added that the focus on free school meals as an indicator for deprivation counted against schools in f40 counties as there was a low take-up of FSM in rural areas.
The letter was supported by heads and school business managers in some of the most poorly funded areas.
Roger Hale (pictured, left), headmaster of Caistor Grammar School in Lincolnshire, said he has very few pupils on free school meals in a school in one of the poorest-funded counties in the country. "We are probably the least deprived school in the country. I think we receive about #163;800 in pupil premium money," Mr Hale said. "At the moment, the pupil premium is only making about a 3 per cent impact on schools' budgets.
"But the pupil premium is doubling over the next three years, so 3 per cent becomes 12 per cent and that is a sizeable amount of money. For some schools that could be #163;70,000-#163;80,000, which buys you three teachers. I can't afford three days of a teacher."
Sandy Woodcock, finance and facilities manager at Ribston Hall High School in Gloucestershire, said she understood the need for spending more on deprived pupils, but added the baseline funding to schools should be fairer. "We are very, very low on the funding ladder but it is something that we have had to manage with. It does make it hard, however, when you look at some counties and you see they are getting more than #163;1,000 extra per pupil," Ms Woodcock said.
Heads' union the Association of School and College Leaders, said it understood the f40's concerns around funding, but pointed to evidence that showed how big an effect the pupil premium is having.
"We have a significant amount of evidence on how people are spending the pupil premium, and it shows it is being used to very good effect to improve standards in attainment," Malcolm Trobe, ASCL's deputy general secretary for policy, said.
"But the bottom line is the current distribution mechanism works against a number of local authorities who are poorly funded."
The Department for Education admitted current school funding was "flawed", adding that it was working to create a fairer and more transparent system. But it argued that it was too early to draw "sweeping conclusions" about the pupil premium.
Research released last month revealed the Government's plans for a new funding formula would lead to schools in some of the country's most deprived areas suffering 10 per cent cuts to their budgets.
A report by the Institute for Fiscal Studies said the least disruptive change in the way schools were funded would lead to schools in areas such as Liverpool, Wigan and Coventry having their budgets cut by 6 per cent on average and possibly up to 10 per cent.
"Any change would also bring costs and disruption with large losses for some schools," Luke Sibieta, IFS senior research economist, said.