Earlier this year pound;1.5 million was earmarked to support the education of newly-arrived pupils who have been dispersed around the country by the Government.
Schools get up to pound;500 for each refugee child to pay for the additional costs of language support.
The latest Home Office figures show that about 6,000 people were dispersed to the "cluster" areas. The North-west and North-east, Yorkshire, Humberside and Scotland have taken the bulk so far.
But more than a third of new asylum-seekers have refused to be "dispersed" and remained in London and the South-east.
Schools in these overburdened authorities, including Newham and Haringey which are already educating thousands of refugee children, do not qualify for the government grants because they are not dispersal "cluster" areas.
Graham Lane, chair of education for Newham, said: "If schools in Newcastle needthis money, so do schools in Newham. We have people arriving all the time and it is costing local authorities thousands of pounds."
Marion Rosen, head at Star primary in Newham, which took 30 asylum-seeking children last year, said the money was essential to provide the children and their families with the support they needed.
The Refugee Council and the Children's Consortium on refugee children, made up of voluntary-sector organisations, have also questioned the anomaly.
A spokeswoman for the Department for Education and Employment said: "The money is aimed at building up expertise and infrastructures in language support in areas which are unused to dealing with asylum-seekers. We are keeping the issue under review."
In April, an estimated 2,500 asylum-seeking children had no school place. The figure has dropped substantially, according to the Refugee Council, although about 130 children in Haringey and just under 100 in Newham are still on waiting lists.