Contractor Pihl UK is building the new Cowes Enterprise College.
The job has been hit with delays due to bad weather and will not now be ready until next spring – six months later than the original completion date.
The council has now assembled a new project management team to oversee the scheme.
Council chief executive Steve Beynon told the Isle of Wight County Press: “Two members of council staff have been suspended, as a precautionary measure, pending the outcome of an internal investigation into the management of the contract for the Cowes Enterprise College build.
“The council’s overriding priority is to ensure the new school building is complete, safe and ready to be used as soon as possible.
“To make this happen, a new project team has been assembled, drawing on experience from across the local authority.
“The responsibility for schools capital and assets has been transferred to the directorate for the economy and environment.
“The governing body and trust of Cowes Enterprise College have been kept fully informed of these developments and we continue to work closely with them.”