Biosecurity Minister Damien O'Connor said farmers were improving their on-farming biosecurity by making greater use of the National Animal Identification and Tracing (Nait) scheme.
Changes were being made to ensure Nait was easier to use and a more effective biosecurity tool following its poor performance during the M. bovis outbreak.
While hundreds of warning letters and more than 70 fines had been issued to those breaking the rules, thousands of farmers had raised their game, Mr O'Connor said in a statement.
Mr Holgate said while sheep and beef farmers could expect solid farm-gate pricing in the coming year, they would be wise to keep a close eye on local issues which had the potential to affect on-farm production costs and productivity.
New regulations relating to water quality, indigenous bio-diversity and greenhouse gas emissions were expected in the short-to-medium term and farmers would need to look carefully at the detail of any incoming regulation to ensure they understood how it was likely to affect their operations, what investment would be required to meet new targets and how any investment could be leveraged.
Sourcing labour was another issue affecting the red meat sector supply chain. Both farm owners and meat-processing companies had had some difficulty sourcing workers this year.
With labour availability expected to remain tight next year as a result of low levels of unemployment and restricted access to migrant labour, there was scope for that to affect producer and processor productivity, he said.
Total animal protein production growth - across all terrestrial and aquatic species - was expected to continue to increase next year, although the rate of expansion was slowing.
Global animal protein growth below the five-year average was forecast for 2019, after stronger-than-expected growth this year.
Pork and wild-catch seafood were expected to see the largest declines, although the slow-downs in poultry and beef growth were also material.
A shift to protectionist policies and US dollar strength meant there was a lack of clarity regarding next year.
The US-China trade war had reshaped pork and seafood trade this year and, as major players in the global animal protein trade, their disagreement was having much wider implications.
Of most significance for New Zealand sheep and beef farmers was the affect of the trade war on beef trade flows.
"While we do not see any direct beef trade between the US and China in 2019, we do see US exports looking for new destination markets and this has the potential to distort other trade flows.''
Global feed prices were set for a gradual increase in 2019, supported by robust demand against a backdrop of tightening supply.
Those higher prices would help to improve New Zealand's competitiveness compared with other key exporters of animal protein, particularly beef.
"Given New Zealand's minimal use of feed in comparison to our export competitors for red meat products, an increase in feed costs is likely to more significantly lift our competitors' overall cost of production and create a comparative cost advantage for New Zealand.''
