This was the public spending watchdog's first review of the £9 billion criminal court system which examined how the Crown Prosecution Service, Home Office and Lord Chancellor's Department interact.
The NAO found nearly 750,000 magistrates' courts cases each year have to be adjourned because of errors by participants.
This can delay cases by more than two weeks per case which costs around £40 million.
Crown court cases that fail to go ahead, the report says, cost £44 million per year.
The report points out that judges and magistrates are failing to use the sanctions available for punishing those who cause the delays