It says in first quarter of this year, only 37% of truancy cases were resolved within ten days, compared with an Education Ministry target of 90%.
The ministry this year combined two different types of truancy service, reduced the number of organisations providing the services and increased spending from nearly $6 million a year to $9 million.
However, in some regions school principals say the changes have left them with a much worse truancy service.
Post Primary Teachers Association president Angela Roberts told Nine to Noon the shift to the new system has gone badly.
She says the contracts were not signed until January, the computer system was not ready to go live and the key performance indicators the providers must report against are difficult.
"So the whole thing's a mess, the providers are actually nobbled in the process," she says.
Ms Roberts says many of the new services are finding a much higher level of difficult truancy than the ministry told them to expect.
Porirua College principal Suzanne Jungersen says changes have left her school worse off.
She told Nine to Noon the service in her area now has fewer staff working on truancy and does not deal with difficult cases.
The Ministry of Education says the new service is still bedding in and it will review the system at the end of the year.
Hear more about the new truancy system on Nine to Noon.