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.
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.
