She recently presided over the publication of a green paper on special needs education and was keen to hear the views of the charity, which represents more than 70 families of children and young people with autism spectrum conditions in the borough.
Runcorn MP Graham Evans arranged the meeting and also gave the group a tour of the Palace of Westminster.
Ciaran Shanahan, HAFS development manager, said: 'It was very encouraging to hear the minister's comments – which were supportive of increasing the statutory powers of parents to make decisions about their children's futures.
'We look forward to more discussions with The Department for Education regarding our proposals, including the possibility of setting up an autism specific free school in Halton.'