Ministers have ordered a school to cut its links to the Barnfield Federation, which is currently under investigation.
Parents at Sandy Upper School were informed of the decision this week.
The federation was placed under investigation in November by the Department for Education (DfE) because of issues over its finances and management.
Sandy Upper was taken over in September and as a result some students were forced to drop their GSCE options because the federation wanted them to concentrate on maths, English and sciences.
One parent, who wishes to remain anonymous, said: “Parents are in uproar over this. Some pupils have had three uniforms in three years now and had to change their GCSE options. It’s an absolute shambles.”
Since the investigation was announced, the former head of Barnfield, Sir Peter Birkett, has resigned.
A DfE spokesperson said: “Ministers have decided to pause the expansion of the Barnfield Federation. As a result, the proposed sponsorship of Sandy Upper School by the Barnfield Federation will not be proceeding.
“We are working closely with the governing body to ensure that alternative sponsorship arrangements are put in place quickly. We are determined to ensure the children at Sandy Upper School get the best possible education.”
On Monday, Education Secretary Michael Gove was challenged by Luton South MP Gavin Shuker, who asked if reports into the investigation would be published.
Mr Gove responded: “Very serious allegations have been made in connection with the Barnfield Federation. They are currently being investigated and nothing I say, do or publish should prejudice those investigations.
“However, as has always been the case, whenever there is information it is right we should share it with those affected and with the public, we will share it in due course.”