Over 24,000 learning support assistants have been appointed to help pupils with special needs in English mainstream schools but Dr Farrell described their status as "appalling".
His study for the Department for Education and Employment showed that most are on temporary contracts at little more than pound;7,000 a year and are typically appointed to support children with statements (Records of Needs in Scotland). They are paid only for school hours.
Dr Farrell said he had never come across such an enthusiastic group of staff, although a central issue for inclusion was their training, management and support.
Assistants in the classroom could also create another form of segregation, he warned.
"Inclusion is not about a child with a learning disability in the corner of the classroom velcroed to an assistant all day long. That child could be just as segregated as in a special school," he said.
Dr Farrell believed the assistant had the subtle task of integrating children into groups.
"Pupils themselves do not like having this person stuck to them all day," he said.
About half the pupils interviewed for the study wanted individual sessions to be held outside the classroom, although they wanted to be broadly included in class.
"The key factor is consulting the pupils. Do not assume you know best. Pupils will have a view," he continued.
A major barrier to further inclusion, Dr Farrell warned, were performance league tables. Schools were worried that pupils with disabilities would have a major impact on results.
Children with emotional and behavioural difficulties presented the most challenges for integration policies because of the ripple effect in schools, he added.