Mr O'Connor blamed the previous government's inaction, and lack of enforcement and promotion of Nait, for creating major issues in hunting down M. bovis.
"We will make changes to the Nait system."
A cull of 22,000 cows was now under way and nearly half of those animals had been destroyed, he said.
A cull was necessary to reduce the disease's spread through the national herd.
Farmers whose properties were under control restrictions faced a difficult time, he said.
"I am working hard to ensure the Government and sector make the best possible decision with the best possible information.
"I expect that decision will come in the next few weeks."
Farmers should ensure any compensation claims they made related to M. bovis were accurate as it made the process faster. MPI and Dairy NZ had boosted the number of people working directly with farmers to assist in that process.