A report published last week by the National Audit Office, parliament's spending watchdog, found that construction costs had escalated from £650m to an estimated £933m.
Sir John Bourn, head of the NAO, said the MoD had agreed to fund most of the cost increases. He said: "Departments need to learn the lessons from this project and minimise the risk of this happening in the future."
The NAO report said the MoD should allocate risk to the contractors best able to manage it. It recommended that where a project is considered to pose a significant risk, MoD officials should draw up contingency plans to deal with the risk.
The report said that all parties in a project should be made to understand the elements of a project that were crucial to success at an early stage. It said: "Departments should recognise the potential difficulties involved in capitalising overspends on capital projects."
Although estimated at £650m in February, the facility was originally supposed to cost £237m. Some project observers believe the scheme could crash through the £1bn barrier.