The recent flurry of government announcements about academies and free schools was accompanied by the trumpeting of now familiar themes – autonomy, liberation, devolution of funds to the front line and the banishment of bureaucracy.

A few weeks before Michael Gove issued his latest call to arms, Sir Bruce Liddington, schools commissioner in the last Labour government, now director general of the academy chain E-ACT and one of the movers and shakers in the academy world, made a speech in which he set out his vision for a "world-class education system".

The words freedom and empowerment didn't appear much. Instead, the emphasis was on government grants to charitable trusts running chains of schools, operating in networks, with centralised back-office services, and the possibility of making a profit in the longer term. In one particularly revealing passage, Liddington unveiled his organisation's five-year business plan. From a low base – 11 academies in 2010 – the group has big ambitions. By 2015, it hopes to have 40 academies, 21 free schools and 65 "converter" academies. Elsewhere, he has been reported as speculating that E-ACT might one day run more than 250 schools.

The vision of an education system in which thousands of autonomous institutions bloom, nourished by total control of their budgets has, superficially at least, been the holy grail for politicians on the right for almost 20 years.

But scratch the surface and an alternative vision of the future emerges, one in which a patchwork of government-funded chains, each with a distinct brand, run thousands of schools, top-slicing revenue in the same way that local authorities have been doing for years, and so protected from the public gaze that the outgoing Ofsted chief, Christine Gilbert, recently urged ministers to bring them within the inspection framework.

As you walk into the atrium of the King Solomon academy, a new 3-18 school in north London run by the education charity Ark Schools, the most notable feature is a large overhead banner that proclaims: "Climbing the Mountain to University".

The Ark chain has high expectations of the schools it has been slowly acquiring since Labour's academy programme was unveiled over a decade ago. Its secondaries are expected to achieve 80% five A*-C grades including English and maths in five years. Last year, there was a 12% rise in the number of pupils achieving this benchmark.

Lucy Heller, Ark managing director, and Venessa Willms, headteacher of the King Solomon primary phase, are clear. Academy status has brought valuable freedoms, notably the ability to lengthen the school day in areas of high deprivation. But the Ark brand is less about individual school autonomy than a strong corporate vision, close relationships between head office and schools, and very tight quality control managed from the centre.

Its "six pillars" – high expectations, good behaviour, depth before breadth, small schools, excellent teaching, and longer school days – are rolled out meticulously from the heart of the Ark operation. Every school receives a termly or bi-termly monitoring visit from either of its two directors of education, one of whom is Sir Michael Wilshaw, also headteacher of the Mossbourne academy in Hackney, east London. The directors then feed back direct to the governing body (the majority of whom are appointed by the trust), often without the headteacher present.

The Ark Trust claws back 4.5 % of the schools budget for central services such as HR, procurement, finance, school improvement and research into pedagogy. Heller describes the Ark approach as one of "stewardship" rather than control. "Every school has its own very distinctive character, but all share an Ark vision and ethos. We see our schools as a shared social good for which we currently have responsibility. I am happy that academy chains recognise their accountability for results. There needs to be something, apart from Ofsted, standing between schools and outright failure."

A similar approach is being followed by other large academy groups, although the Reverend Steve Chalke, of Oasis Community Learning, which also retains 4.5% of its schools' funding to provide central services, dislikes the term "chain".

"It isn't a word we would use," he explains. "We prefer to see ourselves as a family of academies. Our aim is to give opportunities to young people who don't currently have them and we believe we do that better if we belong to a family. We started with one school, but realised that we could bring more value by adding more schools. If you build a cluster, you share expertise, costs, procurement and can move teachers around. Each school is better than it would have been by itself."

So what is the difference between an academy chain and a local authority? Heller suggests that many local authorities are too big to permit the relationships and monitoring on which Ark insists, and may lack high enough expectations, although listening to her describe the Ark model I found myself wondering whether many councils would be brave enough to exercise such extensive influence at a time when they are being publicly demonised for bureaucratic control.

The amount councils retain from school budgets varies hugely. Some take as little as 3%, others up to 10%, and some have found new ways to bring about dramatic school improvement. The Learning Trust, a social enterprise that has run education on behalf of Hackney Council for 10 years, has seen GCSE results shoot up in a once-demonised London authority where schools have now regained the confidence of many local parents.

Alan Wood, director of children's services in Hackney, says: "A partnership of local authority, parents and schools can work together to embrace a diversity of autonomous schools, including academies, and still raise standards for children and young people in our communities."

Moreover, the moral purpose articulated by chains such as Ark and Oasis may risk being compromised if other more hard-headed and entrepreneurial groups enter the field. The accounts of the bigger chains, published on the Charity Commission website, reveal how much funding is at stake, and how little transparency exists about the flow of money between the governing trust and the schools, many of whose budgets are not publicly available.

Both Ark and Oasis saw their central budgets increase from around £3m in 2006 to £117m and £70m respectively in 2010, as they acquired more schools. The income of E-ACT increased from £15.5m to almost £60m between 2009 and 2010. And the United Learning Trust, which the Labour government had decreed was not fit to take on more academies, saw its income rise from £60m to £138m between 2006 and 2010.

Even if 95% of the central grant is passported to schools – no more than an efficient local authority might devolve – that leaves a handsome sum in the hands of the trust, with scant detail about how the central funds are spent. Eyebrows were raised when it emerged that Liddington's own salary had risen from £154,000 in 2009 to £280,000 last year (thought to be over £300,000 when pensions and bonuses are included). The E-ACT director general now earns more for running 11 schools than many council chief executives receive for overseeing multibillion-pound budgets, and almost double that of his paymaster, the education secretary, Michael Gove. The accounts of E-ACT, which retains 5% of its schools' budgets, also reveal that it pays trustees for consultancy work and is now setting up a for-profit arm, E-ACT Enterprises, to sell services back to schools, althought profit will be ploughed back into the charitable arm. Even without the potential to make a profit, the financial returns to those involved in school chains can be considerable.

For some, the discreet Department for Education brokering of deals between academies, free schools and chains is the clearest sign yet of a long-term goal to allow profit-making schools. Martin Johnson, deputy general secretary of the Association of Teachers and Lecturers, says: "We've argued for some time that many academies would struggle to go it alone and would turn to a new friend. We also predict a tendency for these friends to be swallowed up by large organisations, and ultimately by the private sector. A relaxation of the prohibition on profit is sure to follow."

According to a DfE spokesman, there is "no limit" to the number of schools that can be taken on by a chain if it is perceived to be doing a good job. "The secretary of state would also say it is up to the chain how they manage their funds and how much they retain for central use," he adds.

But Heller is more guarded about how the policy should develop over the longer term: "There need to be tough decisions about who the schools are given to," she says. "And Ark would always balance the desire to take on more schools against the risk of losing the personal relationships that are crucial to our success."

Only time will tell how many academies will end up in the hands of the chains and whether that will have a transformational effect on school standards. In the meantime, it is worth asking whether it is really autonomy that schools need, or smarter forms of local accountability, and who will hold the new breed of chains to account for the large amount of public money that may flow through their hands in years to come.