Robert Lanwarne, the chief executive, said: "Where there are tensions, we have tried to ease them. There are pressure points and the new funding regime is hitting home. We are trying to smooth the way."
Essex, Kent and Hillingdon ,which have large number of GM schools, are among the areas where the FAS anticipates tension between the GM schools and their local authorities.
The Department for Education and Employment has also been warned that some of the new unitary councils, which came into being after GM schools, could be a problem.
A DFEE local authorities support unit, based in Darlington and headed by Elizabeth Wylie, a former education officer, will act as an arbitrator of disputes in the new framework of schools.
Graham Lane, chair of the Local Government Association, said: "The diplomatic corridors have been opened between the two sectors and we have warned local authorities against taking revenge on former opted-out schools. The problem is a minority of GM schools are continuing as if the civil war is still on."
A new organisation, the Foundation and Voluntary Aided Schools' Association, was described by Mr Lane as the GM movement in exile. But Pauline Latham its chairman said: "We have got to move on. We are not rehearsing old agendas."