A review of the Nait programme started in 2016 under the previous government.
It was scheduled to be completed in March 2017 and Mr O'Connor said he was recently given a final report after he asked for its completion.
''Given what we've learnt from the Mycoplasma bovis response, I was concerned that this report had not been finalised and released,'' Mr O'Connor said in a statement.
The Technical Advisory Group (TAG) helping with the disease response, and investigators tracing animal movements on the ground, made it clear the lack of accurate records for animal movements in Nait had complicated, and slowed, response efforts, he said.
At one farmer meeting, Ministry for Primary Industries director of response Geoff Gwyn said Nait had fallen short of MPI's expectations and, if it had been a fast-moving disease, then there might have been a very different scenario.
The recently released TAG report said it was the first time the animal traceability system had been used for one of its primary purposes.
Its value was limited by the failure of many farmers to fulfil their responsibilities under the system, making the tracing of animal movements far harder and less reliable than it should have been.
The report detailed a major review of Nait with 38 recommendations aimed at streamlining processes and boosting access and compliance.
Recommendations included enabling direct access to Nait core data by police and other crown agencies to support stock theft and wandering stock inquiries.
Another was for the addition of other attributes in response to farmer and/or industry requests to support disease management, food safety, marketing assurance and animal production needs.
Federated Farmers president Katie Milne said anything that could be done to improve the system and make it more effective and easier for farmers to use would be valuable.
The TAG report said there had to be a substantial improvement in compliance by herd owners, as well as making some changes in reporting procedures, to ensure Nait fulfilled its objectives more effectively.
Mr O'Connor said the Nait review raised several issues: a lack of up-to-date information of cattle location; the need for enforcement, which had been ''non-existent'' for people failing to use the system; inconsistencies across data sets because of multiple farm IDs; the need for more resources to operate Nait: a lack of appreciation regarding the need for a tracing system despite New Zealand's high economic dependence on cattle; and that Nait was behind systems used internationally, especially in Australia.
A consultation process would start soon so farmers and industry could have their say on how to improve Nait.
Ospri, which manages the programme, said New Zealand's agricultural sector would ''benefit significantly'' from implementation of the recommendations arising from the review.
