In February the education select committee called on the Department for Education (DfE) to end the ban on local authorities creating multi-academy trusts by allowing councils with a strong track record in education to establish academies.
But in its response to the committee's report on multi-academy trusts (MATs), the department said such a move would undermine its academy schools policy.
"It is important to maintain the independence of academies, for example in setting the curriculum, pay or school hours," the DfE response states.
"This is a crucial part of encouraging the innovation that has driven up standards in so many schools. This is why we do not allow academy trusts to become subject to the influence of a local authority."
The DfE added that it encourages all academy trusts to work with local authorities and that council representatives can join academy trust boards, although they cannot make up more than 19.9 per cent of those boards.
Elsewhere in its response, the DfE also rejected the committee's call for Ofsted to carry out full inspections of MATs in addition to its inspections of individual academy schools.
"The department does not accept that there is a gap in assessing the quality of MATs' education provision," said the DfE.
"It is right that Ofsted's starting point in their work with MATs continues to be the inspection of individual academies."
However, the DfE said it would work closely with Ofsted to consider possible changes to the inspection regime as the school system evolves.
On the committee's recommendation that action is taken to ensure academy schools are accountable to and better engage with parents and local communities, the DfE said it is "vital" that the governing boards of MATs connect with local people.
"We do not want to see boards become detached, distant or unanswerable to parents," it said.
The DfE said measures are already in place to avoid this happening, including the requirement for academy trusts to reserve places for parents in their governance structure. Parents and pupils who feel their academy trust is not listening to them can raise their concerns via the government website, it added.
Kevin Courtney, joint general secretary of the National Education Union, said the DfE "should hang its head in shame at this response".
"To claim that multi-academy trusts are held accountable at all levels and that the department holds trusts to account and intervenes swiftly when problems arise is a grotesque parody of the real situation," he said.
"The reality is that there is no accountability within the academy system. Unaccountable trustees make decisions about the running of schools with no accountability to parents or communities. Regional schools commissioners appear clueless about what is happening in MATs in their region, and even when problems are pointed out to them they are unwilling to act."
He said academy schools should be returned to "their local authority family of schools" to ensure democratic accountability.