The Tories have pledged to stop the closure of special needs schools.
Mr Howard said many parents felt the system worked against them
Parents face a clear choice between a Tory government who would support special schools and Labour who would close them, Michael Howard said.
The "rigid approach" of educating all pupils in mainstream schools ignores children's uniqueness, he said.
Labour says Tory plans to cut £35bn in spending would hit education. The Lib Dems said the debate should be about what is best for individual children.
Outlining his party's approach, Mr Howard said the "inclusion at all costs" culture had undermined teachers' authority and hit school standards.
Parents across the country were fighting to keep their child's special school open, Mr Howard said.
"They fight to keep special schools open because they understand how good these schools are for their children.
"Parents value the expertise and experience of the teachers. They see the progress their child is making and they do not want to lose this."
The Special Educational Needs and Disability Act 2001 states that a child must be educated in a mainstream school unless this is "incompatible" with parents' wishes or interferes with other pupils' education.
Mr Howard says a Conservative government would revoke this presumption as it had led to the closure of many good schools.
"Some parents lack confidence that mainstream schools will offer the support that they need, but they know that special schools will provide it."
He also said that teachers lacked guidance on dealing with special needs children.
Education Secretary Ruth Kelly said parents of children with special educational needs would be among those hardest hit by Tory plans to cut £35 billion from public services.
"The Tories would introduce a voucher system that would cut over £1bn from state schools to subsidise the private education of a few.
"How would a £5,500 voucher pay for a child with special educational needs that might cost up to £200,000?"
Labour also pointed out there are 90,000 pupils in special schools.
Liberal Democrat education spokesman Phil Willis said he was saddened to hear "more talk of compartmentalizing our school children".
The Tories say parents value the expertise of specialist teachers
But acknowledged that parents of children with special needs deserved to know they were being taught in the most appropriate setting.
Thousands of children, who previously would have automatically gone to special schools, had been "successfully educated with their peers in mainstream schools," he added.
Moves to close special school began under a Conservative government but 91 have closed since 1997 - leaving the current number at 1,148.
Department for Education and Skills said parents had a right to a special school place if they wanted it and that consolidating provision in fewer, bigger schools meant there were more "centres of excellence".
The department recently announced that a dozen special schools, state and private, would have specialist status with extra money and a remit to spread good practice.