"I have heard suggestions that the approach to setting targets will cause schools to take a less inclusive approach to children with special needs, " Helen Liddell said.
"It is suggested they will be left behind as schools focus their attention on children who can make a difference to the achievement of the target.
"I believe this is a false concern. Not only is it insulting of the professionalism in schools, but it ignores the fact that schools have been invited to set their targets in the light of their own estimation of their circumstances. This will give them the opportunity to take full account of the special needs population that they serve.
"This is not the concern in relation to targets. The concern is to ensure that special needs children benefit equally from the focus on improvement that target-setting is designed to stimulate."
Mrs Liddell said the individualised educational programme to be introduced for each child would be particularly relevant for special needs. The Inspectorate is to issue guidance on this early in the new year.