The head of a highly regarded independent school has stood down from leading a new academy after falling out with its Christian sponsor.

The Rev Tim Hastie-Smith, chairman of the Headmasters' and Headmistresses' Conference, which represents 250 leading independent schools, has decided to withdraw as principal of Kettering Academy, which is due to open next year. The academy's Christian backer, the United Learning Trust was upset by Mr Hastie-Smith's decision to employ a teacher who had secretly filmed a pupil having sex while on a school trip.

The teacher, Michael Clarkson, was struck off the teaching register last week. Mr Hastie-Smith had given him a job at Dean Close School in Cheltenham five months after the incident because he believed in “ giving people a second chance”.

Mr Hastie-Smith was due to leave the independent sector and become the head of the academy when it opens next September. Yesterday he said: “It has become clear to us all that, if the Kettering Academy project is to prosper, it would be better if I were to withdraw. It is far more important that this academy succeeds than that I should be its principal.”

The academies programme appeared to suffer a setback this week when Lord Adonis, the former Schools Minister and champion of academies, was moved to the Department for Transport in a reshuffle.

More than 80 schools have become academies, but Lord Adonis wanted to exceed the target of 400, with a huge expansion of the project. The future of this ambition is now in doubt.

In another blow to the programme, a company is preparing to withdraw its sponsorship of an academy in Middlesbrough. It would be the first time that a backer has pulled out of the scheme, in which companies or organisations support academies, state schools that are semi-independent from local authority control.

Amey, a support services company that works with the defence, aviation and transport industries, admitted yesterday that it was “discussing the future of its sponsorship of Unity City Academy in Middlesbrough with the Department for Children, Schools and Families”.

The company, which had a turnover of £1.37 billion last year, and made a profit of £75 million, paid £2 million to sponsor the academy when it opened in 2002. With shockwaves from the credit crunch being felt across the business world, it is likely that Amey is trying to cut back wherever it can. The company is part of Ferrovial, which reported a debt burden last month of £23 billion. Ferrovial owns seven British airports but was ordered recently by the Competition Commission to sell Belfast, Gatwick and Stansted.

Amey is also the majority shareholder of Tube Lines, which manages three Underground lines. It has committed to spend more than £4.4 billion over seven years.

Unity City Academy opened with a great fanfare in 2002, becoming one of the first academies outside London.

Yesterday a company statement said: “Amey's expertise is in managing change and improving organisational efficiencies, and we felt we were in a strong position to support UCA in overcoming its challenges when we became involved in 2002. We are now working with the DCSF to identify the best way forward and establish how to build on the improvements that have been achieved to date.”

The school was one of the 638 named as underperforming by Ed Balls, the Schools Secretary, this year. It failed to meet the target of 30 per cent of pupils achieving five good GCSEs, including maths and English.

Robert Dore, the principal of Unity City Academy, told the Times Educational Supplement: “This situation has never occurred before, so if it goes ahead, we don't know what it will mean for the school. I am extremely concerned, but we will not let it affect the pupils here, who have made tremendous progress.”

Half of the school authorities in England are infringing the new admissions code, which was introduced to tackle “back-door selection” by state schools.

Sir Philip Hunter, the chief adjudicator, said yesterday that some schools were still asking about parents' marital and occupational status on application forms, while others continued to demand that parents make them their first preference, even though this is no longer allowed.

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