A question mark is hanging over building work at the Isle of Sheppey Academy after the government confirmed huge cutbacks to a programme that was to have seen millions of pounds spent on transforming outdated premises.

The dual-site Academy, made up of the former Minster College secondary school in Minster Road and Cheyne Middle School in Sheerness, is one of 40 schools in the county that could be affected.

Education Secretary Michael Gove labelled the Building Schools for the Future programme “dysfunctional” and “unnecessarily bureaucratic” when he announced it would be stopped this week.

While some schemes have been called off completely, the Academy is one of eight in the county that is “under discussion”.

However, Kent County Council refused to reveal when a decision would be made, what savings were being looked at and if both the East site at Minster and West site at Sheerness would be affected.

The £54 million Sheppey Academy has, in its short history, already been hit by building setbacks. Islanders were promised that “distinctive and stunning” buildings would be ready by September this year.

But the Times Guardian revealed in February that after one of Kent County Council’s original partners pulled out, the buildings would not be ready until September 2012.

KCC leader Paul Carter said he was surprised and disappointed at the government announcement. He added: “I appreciate that all those involved in the project, from head teachers to contractors, will also be disappointed. We need time to take stock of our position and reflect on the announcement.

“I would like to see all the people involved coming together to talk about innovative ways of revitalising secondary schools. We stand ready to offer any assistance to the government’s review panel.”

The huge reduction in the scheme has come under fire from opposition parties and teaching unions.

Christine Blower, the general secretary of the National Union of Teachers, said there was “no excuse for leaving schools which were promised new buildings swinging in the wind. Poor learning environments have a negative impact on the education of children and young people”.

The announcement came just two weeks after Academy principal Dr Paul Mortimer revealed he would be retiring on August 31, before the school opens for its second year.

• Building Schools for the Future was launched by the previous government in 2003. The aim of the £55 billion government programme was to rebuild or renew every secondary school in England. Kent was expected to benefit from £1.8 billion worth of investment for new schools.