Ron Jacobs, acting manager of the department's school diversity division, told MPs that parents with several specialist schools nearby would have greater choice, but it would not be the same for families who lived in rural communities.
"Some parents will be able to see this as providing more choice but the department does not dispute the fact that it does not apply across the country," he said. "In many situations it will not enhance choice."
The comments came in response to questions by the Commons education select committee, which asked if the DfES would support transport so that pupils in rural communities could attend a specialist school, such as a performing arts college.
Mr Jacobs said that over five years the Government had come to see specialist schools less as a creator of parental choice and more as a force for general school improvement.
However, Education Secretary Charles Clarke mentioned greater choice as one of the benefits of specialism when he announced in November last year that all schools would be able to gain the status.
Professor Ron Glatter, of the Open University, said that available evidence did not show a widespread parental demand for diversity between schools, and that there were indications that a "pecking-order" of specialisms was developing.