Jarvis agreed the firm had had problems with subcontractors but said they were not a cause of delay. The firm added that a large part of the delay had been due to discovery of asbestos in the schools.
Wirral council said that asbestos was found in one school where it was not expected. It said Jarvis was given extra time to deal with it.
The council blamed the delay on other factors, including the firm's difficulties recruiting labour and problems with subcontractors.
The project ran into trouble at the start of this term when five of the schools it covered were unable to open on time as a result of work not being completed.