More than half of England's local authorities are involved in the scheme
Almost two-thirds of the early waves of school rebuilding projects in England are behind schedule, figures obtained by the Conservatives show.
Some 24 of 38 Building Schools for the Future (BSF) projects are delayed, data from a parliamentary answer reveals.
Recently it emerged that only 37 schools would be completed by the end of 2008 compared with the 200 originally planned.
The government said the programme was now accelerating rapidly.
It has been known for some time that there have been problems with the government's plans to rebuild or refurbish every secondary school in England.
As the building gets more and more behind schedule, the costs are rising all the time
Michael Gove Shadow Children's Secretary
But ministers and officials have been circumspect about the scale of the delays affecting the BSF projects.
These new figures show 76% of local authority projects in the very first wave, 70% of those in the second wave and 42% in the third wave of the scheme have fallen behind their original timetables.
These were the areas which the government deemed in most need of school redevelopments.
A detailed analysis suggests projects in three areas have slipped more than two years behind their original target completion dates and a further eight are facing delays of a year of more.
But the parliamentary written answer does not address any possible delays in later BSF schemes, which is now in its sixth wave.
Shadow Children’s Secretary Michael Gove said the government was failing to deliver on its flagship education project.
"As the building gets more and more behind schedule, the costs are rising all the time.
"[School's Secretary] Ed Balls’s department simply doesn’t seem capable of handling large-scale projects like this. It is teachers, parents and children that are missing out as a result."
Schools minister Jim Knight said: "While this government is committed to rebuilding or refurbishing every secondary school, the Tories have pledged to slash our school building programme by £4.5bn.
"This would mean cancelling one in seven future school building projects - a total of 360 schools. Instead of criticising the BSF programme Michael Gove should come clean about which schools would no longer be rebuilt if the Tories had their way."
A spokesman for the Department for Children, Schools and Families said: "The fact is 35 BSF schools are now open and the programme is now rapidly accelerating so that over 200 new or refurbished schools will be opening a year by 2011.
"By 2020, we expect most local authorities to have completed their full BSF programme.
"The remaining authorities will already have some new and refurbished schools completed and be in the final stages of renewing their remaining estate."
Time-lapse footage shows a school being built
He added: “We have been upfront about delays in the programme and taken action to address the key challenges to delivering this unprecedented building project and to accelerate future waves of the programme.
"The select committee last year reported on BSF and said we were absolutely right to take our time in getting the project right."
Partnership for Schools, which oversees the school rebuilding schemes, insists it has tightened up the management of the scheme and that it now has things under control.
It says that changes to the procurement process have shaved eight months off project completion times and that upcoming changes will reduce this still further.
These changes, however, were brought in too late for the projects in the first three waves of BSF.
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