A second free school has been ordered to close by ministers due to concerns over the quality of education on offer, it has emerged.

The secondary school at the ailing Al Madinah free school in Derby is to shut at the end of the academic year but primary provision will continue at the school, schools minister Lord Nash has said.

It becomes the second free school the Department for Education has been forced to shut - albeit partially - in almost as many months, after the Discovery Free School in West Sussex was told to close its doors in December.

The closure is yet more bad news for education secretary Michael Gove’s free school policy, which is also being dogged by an ongoing criminal investigation at the King Science Academy in Bradford.

Al Madinah, which was the first Muslim free school in the country, has been at the centre of a series of controversies since the start of the academic year, resulting in it being described by Ofsted inspectors as being in chaos on two separate occasions.

And in a letter to the trust released on Friday, Lord Nash said it would be in the “best interests of parents and pupils” to close the secondary school.

“It is clear that there is a great deal of work to do at the school,” he writes. “The feedback I have received from my officials, as well as the findings of Ofsted’s reports, make plain the scale of the challenge facing the trust.

“I am particularly concerned at the poor quality of secondary teaching and the lack of breadth in the secondary curriculum. I have come to the conclusion that it would simply not be in the interests of parents or pupils at the secondary school to continue to fund provision which has failed them in the manner now apparent.

“I have decided it would be in the best interests of those children in the secondary school to continue their education elsewhere from this September onwards.”

The school became embroiled in controversy after claims were made of discrimination towards female students and members of staff, with girls made to sit at the back of the class, as well as concerns around health and safety.

The school was then forced to close for a week during term time in October after its first Ofsted visit, which led to it being threatened with closure by Lord Nash unless it turned itself around.

The leadership of the school was handed over to Barry Day, chief executive of the education charity Greenwood Dale Foundation Trust, which runs a number of academies in the region.

It is under Mr Day’s oversight that the primary school will continue, with Lord Nash stating he was “confident” the new trust will be able to deliver a “high quality primary education”.

“I appreciate that this will be a disappointing decision, particularly for those parents with pupils in the secondary school,” the letter adds. “I believe that acting now will ensure their children receive a much better standard of education than would otherwise have been the case.”

The secondary school will close its doors at the end of the summer term.

A DfE spokesperson said the “vast majority of free schools were “performing well”.

“We have monitored Al-Madinah very closely since problems came to light last year. Based on the current situation we believe the new board - which began work last week - needs to focus efforts on the primary school in order to bring about the level of improvement required,” the spokesperson said. 

“The board has accepted our decision to close the secondary school and we have offered our full support in helping pupils to find alternative places before the start of the next academic year.”

The NUT said Mr Gove had questions to answer over his flagship policy, adding that the programme should be put on hold.

‘The free school programme must be paused so that the lessons of troubled schools such as the Discovery Free School, Al Madinah and the King’s Science Academy can be learned,” NUT deputy general secretary Kevin Courtney, said.

“Free schools should be brought within the responsibility of their local authority to ensure proper oversight of both their governance and the standard of education they offer.