Payments totalling £50m due in October 2002 had not been paid six months later, according to the NAO.
The new IT system was developed through a partnership agreement between the Welsh Assembly and consultancy Cap Gemini Ernst & Young.
Problems included underestimating the amount of testing needed, faults with scanning technology, the creation of a new customer database and Welsh Assembly staff being unfamiliar with the systems. This was compounded by problems in delivering the necessary training programme, the NAO report said.
John Bourn, head of the NAO, said that despite the problems, the IT system should help the assembly deliver improved services to Welsh farmers.