The Otago Regional Council has revised its pest management strategy and, from August 1, the maximum allowable level of infestation will be the same throughout the province at McLean scale three - infrequent sign with buck heaps more than 10m apart with the odd rabbit seen.
Landowners would have until October 2012 to comply.
The council's director of resource management, Dr Selva Selvarajah, said some traditionally rabbit-prone country in Central Otago had previously been allowed to have infestation levels of McLean scale four or five.
"Basically this says the whole of the region is three."
The council estimates that more than 25,000ha of the province will exceed the maximum allowable level (mal) of three.
In 2001-02, after the arrival of rabbit haemorrhagic disease (RHD), 3000ha of Otago exceeded the then mal, that figure split almost evenly between Central Otago and the rest of the province.
The council said the areas most at risk of exceeding the mal were Upper Clutha, St Bathans, Alexandra, Earnscleugh, Cromwell, Roxburgh, Wanaka and parts of the Maniototo and Pig Root.
The new strategy introduced other changes as well.
It required owners of land with a mal of three or more to submit, within two months of receiving a letter from the council, a strategy to reduce the infestation, including methods to be used, areas to be treated and a timetable.
Dr Selvarajah said not to do so was an offence under the Biosecurity Act.
There was also a requirement to have regard for a neighbour's rabbit situation, with work to be compatible or jointly undertaken.
"That means, if your next door neighbour has lower rabbit numbers than your property, you have got to match up or build a fence."
Dr Selvarajah said RHD was still an effective rabbit killer, accounting for about a third of all rabbit deaths, but on rabbit-prone properties, where there was little or no follow up work, it was not as effective.
Serum tests at 10 Central Otago sites revealed about 60% of rabbits had developed immunity to RHD, but Dr Selvarajah said the council believed the level of immunity had reached a plateau.
He said conventional control, alongside RHD, removed rabbits immune to the virus, reducing the proportion of resistant rabbits, which in turn resulted in higher mortality when RHD reappeared.
The council has also found a change in the behaviour of the virus.
Initially it appeared in November-December and April-May, with the autumn outbreak the most pronounced.
Now, the first epidemic was appearing in August, too early for an effective kill, as the majority of rabbits were still youngand carried maternal antibodies that conferred resistance to RHD for life.
There were localised epidemics in December, February and autumn.
Recent night-counts had shown variability in rabbit numbers, ranging from 0.1 rabbits counted per kilometre at Manorburn, where there had been an intensive gassing and night shooting programme, to just over 18 at North Roxburgh where there had been little control additional to RHD.
Properties where one or two night shoots or gassings had been carried out each year, and which had rabbit counts of one to three per km, were where RHD would "have a helpful impact", the council said.
The council-owned pest control company, Regional Services, in conjunction with the council's compliance unit, would assess mal levels, but there was some disquiet among farmers that Regional Services was also one of the major pest contractors in the province.
Dr Selvarajah said any potential conflict of interest would be managed carefully and the council would not direct farmers to any pest control provider.
"Our interest is working them towards a control programme and it is up to them to engage any contractor they like."
Regional Services was separate from the council's enforcement arm, he said.