Kent and Sunderland have confirmed that they are investing council taxpayers' money in the schools, which are supposed to be free of town and county hall interference.
Conservative-controlled Kent is putting some pound;2 million into two academies and Sunderland, a Labour authority, is investing pound;3m in three schools.
The councils' involvement represents a shift for academies, which have provoked criticism because they can control admissions, set their own rules on exclusion, deviate from national contracts for teachers and alter the curriculum.
Concerns have also been raised over the power wielded by sponsors - normally entrepreneurs, faith groups or charities - who gain control of the governing body after making a contribution of up to pound;2m towards buildings.
But now councils are coming forward as sponsors, normally alongside a private third-party backer. Their intervention will deprive some academies of independence, particularly over admissions and exclusion.
Kent county council and Microsoft are sponsoring one academy, investing Pounds 1m each. A similar deal has been brokered between the council and Roger de Haan, the founder of Hastings-based Saga Holidays, for another academy.
In Sunderland, the council will use the same model for three academies. The authority says they will be part of its admissions system but only for children aged up to 16, with pupils going on to Sunderland's sixth-form colleges.
In Birmingham, the council is not sponsoring any of its seven proposed academies but the hung authority will retain control over their admissions.
It says a series of three or four sponsors will invest in each academy, but the authority will effectively run the school.
Headteachers welcomed the developments. John Dunford, general secretary of the Association of School and College Leaders, said: "Some of the early academies were developed in the teeth of opposition from the local authorities. This means academies are going with the grain of local planning, which makes it much easier for them to work together with local schools."
A spokesman for the Department for Education and Skills said all academies were developed after consultation with local authorities and parents, adding: "There has been no policy change. Local authorities have been closely involved and enthusiastic supporters of academies since the beginning as they know academies help to raise standards in areas that have suffered decades of neglect."