Somerset county council has voted to close the centres in the west of the county in April, 2008.
The units are based at Minehead first and middle schools, Ruishton primary, Kingsmead and Court Fields community schools and West Somerset community college.
The council said the schools had received additional funding over the past 30 years, where other schools had not.
The estimated pound;225,000 a year saved will be redistributed across the local authority.
The special needs resource bases, as they are called, were opened in west Somerset in the 1970s. They cater for pupils with moderate learning difficulties and avoid the need for them to make long journeys to schools in Taunton and Bridgwater.
Planning and recruitment Neil Dalton, head of Ruishton primary, said the existing funding of pound;79,000 a year had allowed him to plan ahead and recruit expert staff.
His school has up to 30 pupils with special needs attending on a full or part-time basis.
Mr Dalton said: "What these plans mean is that I will lose expert staff as I won't have the funding continuity. I will still have the same number of pupils but will have to apply for funding for them individually.
"It is a farce. I would have hoped the county council could have emulated our system elsewhere in Somerset. We have an excellent inclusion system which is now under threat."
Somerset plans to move pupils in the units to mainstream schools, with support from a team of specialist teachers working across the area.
A report to the county's executive board said children and young people with special needs across the whole county will now all receive funding in the same way, irrespective of where they live.
It said that the closure will mean that "all pupils who have severe and complex special educational needs will be funded on the basis of individual evidence and audited need".
Gloria Cawood, Somerset county council's portfolio holder for education, said: "There has been full consultation with the six schools and parents and governors during 2005.
"The children currently in the resource bases will be safeguarded through the phased closure arrangements. Additional consultation has taken place with the Somerset Schools Forum, where changes in funding proposals are considered on behalf of all schools. The forum supported closure."
She added that the County Council recognised the relative rural isolation of west Somerset and would be looking to develop a form of specialist provision there over the next two years.