Private government concerns about the performance of its biggest academy sponsor led to plans for a proposed school being abandoned, The TES has learnt.
United Learning Trust (ULT), a Christian charity that runs 17 academies, had been the preferred sponsor to run a new school in Portland, Dorset.
But it has emerged that officials from the Department for Children, Schools and Families told the local council to find a different sponsor because of worries over ULT's performance.
The concerns led the council to drop ULT and appoint Stephen Heppell, a professor at Bournemouth University and an education IT expert.
Since then, two ULT academies in Sheffield have been described as inadequate by Ofsted. In September this year, Sheffield Park became only the third academy to be placed in special measures.
The revelation of the Government's concerns come as ministers launched a new accreditation scheme for education providers running chains of schools.
Organisations will have to gain a kitemark in order to set up academies, federations and trust schools, Ed Balls, the Schools Secretary, announced.
To be accredited, providers will have to prove they have a strong model for improving schools, a track record of improving outcomes for young people and the ability to achieve "transformational change" in their schools.
"As we have seen in the academies programme, strong partners and sponsors can have a huge impact on improving school performance," said Mr Balls.
"I want more of these partnerships, but it is right to ensure that we identify the best-possible providers."
A number of academy providers, including the Harris Federation, which runs nine academies in south London, said they supported the kitemark scheme.
ULT has had considerable success in improving Manchester Academy, which is rated outstanding by inspectors and where exam results have improved significantly.
But the DCSF's concerns about the group's wider performance raise doubts over whether it would be accredited under the new framework.
The problems at ULT also bring into question how standards are monitored and maintained when large numbers of new providers are given control of schools - a key part of Tory education policy.
Michael Gove, shadow schools secretary, said this week a Tory government would provide extra funding for graduates of "elite" teacher training schemes to run new schools.
A paper due to be presented at the cabinet at Dorset County Council next month states: "On 9 July 2008, cabinet agreed to go through to feasibility stage for an academy on Portland.
"At the time the proposed sponsor was United Learning Trust. Concern about the performance of ULT caused Department for Children, Schools and Families officials to ask that we seek a different sponsor."
Since July last year, ministers have signed off three funding agreements for ULT academies.
But with Portland it is understood officials were worried about ULT's mixed record of success and a tendency to impose a "one size fits all" regime that makes it unresponsive to local needs.
The local authority is also understood to have investigated concerns about the group's track-record of removing staff. As previously reported in The TES, more than half of its headteachers have been replaced within two years of schools opening.
This summer, ULT launched a major reorganisation that included the controversial appointment of a former John Lewis manager with no teaching experience to develop its school leaders.
John Bangs, head of education at the NUT, said: "If the Government has concerns about ULT, they should not be turning up in a local authority document.
"We should be made aware up front that they have concerns.
"This undermines the argument that the Government is competent in dealing with sponsors and whether it will reach its target of 400 schools. It says one thing is public and another in private."
John Dunford, general secretary of the Association of School and College Leaders, said: "The great benefit of the new accredition proposals is that it will bring into the open the selection criteria for academy sponsors. Up to now this has been too much of a secret garden."
A DCSF spokesman said: "During the process of opening a new academy, a number of different sponsors are always considered, and the best option for the particular local circumstances is chosen.
"In the particular circumstance of Portland Academy, it was felt that another sponsor was more suitable."