At present, all refugee children are sent to mainstream schools near their families' accommodation, but the Government is to pick four rural spots from a shortlist of eight, to house 3,000 asylum-seekers by the end of the year.
The centres will offer housing, shops, interpreters, legal advice and and education on site. Classes for children will include basic English, while adults will be offered English and IT classes.
"The biggest concern we have about these centres is the education facilities," said spokeswoman for the Refugee Council. "Refugees and asylum-seekers should have the same access to education as all other children. Integration works best at the school gate or in the playground. This segregated education system would undermine that."
She said asylum-seekers would be isolated in the rural locations under consideration, including a disused hospital on the south Wales coast, a former RAF base at West Lindsey in Lincolnshire, and Ministry of Defence land at Bicester in Oxfordshire.
The Refugee Council is also concerned that asylum-seekers may become institutionalised if they have to stay at the centres while their applications are processed, which takes an average of 14 months.
Experience on the continent, where such centres predominate, suggests that they make integration harder.
Sally Price, communications director for Refugee Action, said the present policy was, on the whole, working well, although there had been some problems.
"There have been some teething problems. Asylum-seekers have been sent to cities that have been chosen for their housing facilities rather than their capacity to teach children English as a foreign language."
A Home Office spokeswoman said the existing dispersal system was already putting a strain on schools, often those in the most disadvantaged areas who need most support.
"We believe that putting children who speak little or no English into mainstream schools places a strain on them, their teachers and classmates," she said. "We intend that the accommodation centres will provide a good platform for help with and preparation for integration - not hamper it."