Assembly members approved the controversial pound;13 million Raise (raising attainment and individual standards in education) fund last month.
But they divided down geographical rather than political lines over the fund.
The cash will benefit 614 schools where a fifth or more of pupils are entitled to free school meals.
It is intended to support pupils most at risk of leaving school with no qualifications, via additional lessons, booster classes, and improved links with parents and the local community. But Assembly members from north Wales are furious that their schools, and particularly those in Wrexham, have missed out.
Critics say uptake of free school meals is not a good enough indicator of poverty, and that needy schools have missed out on Raise cash.
Assembly government officials are now looking at other ways of measuring deprivation in schools.
There is also anger at the way the money has been forced through without consultation. John Marek, independent AM for Wrexham, accused Jane Davidson, minister for education, lifelong learning and skills, of feathering her own nest, during a debate in the Senedd in Cardiff Bay.
He said: "I'd like to know how many of the schools in the Cabinet's constituencies have benefited compared with those in north Wales?"
Janet Ryder, Plaid Cymru's shadow education minister, said Ms Davidson had broken with protocol by not consulting with local education authorities over distribution of the Raise money.
Peter Black, Lib Dem education spokesman, said: "The rough and ready way it has been dealt with has been shambolic."
Finance minister Sue Essex said she wished there had been more time to carry out consultations, but added: "It is time we made a start on the blot on Wales's civilised society - underachievement in Welsh schools."