Acknowledging the Cabinet rift which has lead to John Prescott openly saying that they would bring back a two-tier system, Ms Kelly admitted that the plans for a new breed of trust schools were confusing.

Before Ms Kelly’s grilling by the Education Select Committee, Cabinet sources said that Mr Prescott was being excused his breach of discipline even though he has made Tony Blair’s task in pushing through the reforms even more difficult.

Labour MPs were voicing astonishment at his open revolt on an issue that could decide the fate of the Prime Minister. But in a move that was seen as another sign of Mr Blair’s weakened authority No 10 made plain that he was in effect turning a blind eye to an intervention by the Deputy Prime Minister that would have spelt the end for most ministers.

Hardly had Ms Kelly begun when Barry Sheerman, the committee’s Labour chairman, denounced the White Paper as “an extraordinarily poorly written piece of work” that had sown unprecedented confusion among educationists and MPs. “If I was still in university I’d say, ‘There’s some good stuff in this but go over the shape and form — there are too many cooks in this document’,” said Mr Sheerman, a former lecturer.

Ms Kelly admitted that there had been confusion about trust schools, but played down the notion that they were a radical departure from foundation and voluntary aided schools. The Education Secretary insisted that the plans would raise standards, especially for children in deprived areas, and not lead to the return of academic selection. Asked if she recognised the concerns expressed by Mr Prescott, she said: “I recognise them but I am completely convinced that this will not create a two-tier system; in fact it will have the reverse effect.” She added: “When I hear commentators say it’s about bringing back academic selection, they are just plain wrong. We outlawed selection in 1998.”

Ms Kelly said of Mr Prescott’s intervention: “Well, I don’t agree with him. I think this is a good set of proposals that will help the most disadvantaged children in the most disadvantaged areas.”

No 10 made light of Mr Prescott’s attack, published on the eve of Ms Kelly’s crucial appearance before the committee. He had given the interview two weeks ago to Susan Crosland, whose late husband Anthony led Labour’s campaign for comprehensive education, and had expected it to appear sooner.

Mr Blair’s spokesman said that in voicing worries that the school reforms would widen the gap between middle-class and poorer pupils Mr Prescott was “echoing the concerns” other people had expressed.

However, Mr Prescott made clear in his interview in The Sunday Telegraph that he shared some of those concerns, and repeated that in a statement put out on Sunday in an attempt to quell the row. He said that the interview “properly reflects the views that party members have expressed to me as deputy leader, some of which I share”.

Sources close to Mr Prescott said yesterday that he felt able to comment because of the lengthy consultations being conducted by Mr Blair and Ms Kelly between the publication of the White Paper and the appearance of a Bill next year. Privately, though, he was said to be contrite and regretting having given the interview.

He made plain that he was not opposed to the establishment of city academies, one or two of which are to be set up in Hull, the city he represents. “Moreover, they are already established in some of our most deprived areas. I am simply making the point, as I did in Cabinet, that the benchmark against which any reform should be judged is whether it helps children from the most disadvantaged background.”

Mr Prescott said that his concerns should not be taken as fundamental opposition to the whole White Paper, “which continues the major improvements in education since 1997”.

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