"The programme has been hugely challenging for certain farmers that have been impacted by depopulation and I do want to acknowledge that," he told The Country Sport Breakfast's Brian Kelly.
"It has been far from easy. It has been really, really tough."
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It was also important to recognise farmers' financial contribution to the programme - alongside "very significant" Government funding - with 30 per cent of the costs coming from dairy and 2 per cent from beef, Mackle said.
There were many lessons to learn from the experience to ensure a stronger biosecurity process for the future.
An independent review released last year was also helpful as it "didn't sugar coat" what farmers had been through, Mackle said.
"The findings are really helping that both government and industry together are in a better place and are better prepared for a future incursion and it's absolutely vital that we take that review and improve things."
The future of the M. bovis programme depended on these lessons, Mackle said.
"We've got to make sure we absolutely protect the sacrifices and the investments that have been made so far, so it's important that we continue to manage our herds well.
This meant using the National Animal Identification and Tracing (NAIT) programme, he said.
"It's a vital part of our system and we've got to keep getting better at that. There's been a huge improvement there I must say too - which is great."
Other farming countries were watching New Zealand's progress, as the eradication programme was a world-first.
This also underscored what Kiwi farmers had achieved so far, Mackle said.
"I want to say thank you to farmers and all those involved in the programme."
