Construction firm Jarvis has been criticised for its handling of a scheme to build and maintain nine schools.
Schools were unable to open because of the construction delays
The Merseyside project became delayed because subcontractors were not paid, and one firm quit over unpaid bills of £60,000, a BBC investigation found.
Some schools were unable to open on time, prompting anger from parents, said local MP Frank Field.
Jarvis admitted the firm had had problems with subcontractors, but said these were "not a cause of delay".
The spokesman added: "If you were to look at projects all around the country, you would find a lot of highly delighted head teachers, parents, pupils and local authorities."
The BBC's File on 4 programme found that bricklayers had walked off one site because a £60,000 bill had not been settled.
Jarvis also said that a large part of the delay was down to asbestos being found in the schools, which are on the Wirral.
However, Wirral Council says this was only the case in one school, adding Jarvis knew the substance was at other sites and was given extra time to deal with it.
Instead the council has blamed a number of factors for the delays, including the firm's problems in recruiting labour, as well as the difficulties with sub-contractors.
Last month, Jarvis pulled out of day-to-day maintenance on the rail network after criticism of its performance.
The £55m ($91.8m) schools project ran into trouble at the start of this term when five of the schools it covers were unable to open on time as work by Jarvis had not been completed.
The local council has said the delays were "frustrating and disappointing".
Building still remains behind schedule at four of the sites and the deadlines have now slipped to spring next year, the BBC has learned.
During its investigation, File on 4 learned a firm of bricklayers downed tools when its £60,000 bill remained unpaid. Jarvis says the matter has since been settled.
However, news that another subcontractor has withdrawn its labour in a dispute over a payment of more than £1m has prompted fears of even more delays.
File On 4 was broadcast on Tuesday, 11 November at 20:00 GMT on BBC Radio 4 and is repeated on Sunday, 16th November at 17:00 GMT.