It is the latest condemnation for the Digital Media Initiative, which was abandoned in May last year and led to the sacking of its chief technology officer John Linwood.
The NAO said the BBC Executive "did not have sufficient grip" on the IT project, nor thoroughly assessed the system to see whether it was "technically sound".
The BBC aimed to create an integrated digital production and archiving system allowing staff to handle all aspects of video and audio content from their desks. But after years of difficulties during which £125.9 million had been ploughed into it - the plug was pulled.
A report published just a month ago by PricewaterhouseCoopers (PwC) found numerous areas were "not fit for purpose" including governance of the project, arrangements for reporting progress to BBC bosses and risk management.
The report found there was no independent assessment of the technical design to see whether it was technically sound and said governance arrangements for the project "were inadequate for its scale, complexity and risk". Nor did it appoint a senior figure to act "as a single point of accountability and align all elements" of the project.
Diane Coyle, vice chairman of the BBC Trust, said: "It is essential the BBC learns from the losses incurred in the DMI project and applies the lessons to running technology projects in future. The NAO's findings, alongside PwC's recommendations, will help us make sure this happens."