The concerns emerge as more traditionally rabbit-prone land in the Wanaka area is converted into lifestyle blocks.
The issue had been highlighted by problems in getting all landowners in a new Queensberry subdivision to agree.
Council director, environmental monitoring and operations, Jeff Donaldson said there were also concerns about ''reverse sensitivity'' arising from rabbits being poisoned outside the subdivisions moving into those areas to die.
The council had attended resource consent hearings for the Northlake subdivision, on the outskirts of Wanaka, to urge conditions be put in place requiring ''at least'' a perimeter rabbit-proof fence be put around the subdivision.
It had also requested similar measures for the Hidden Hills subdivision, also near Wanaka, where the kanuka stands on the properties were used as a marketing tool offering seclusion for buyers.
''You can see a [rabbit] warren under every stand of kanuka,'' he said.
The concerns were raised at a recent council committee meeting when discussing a report that of nearly 12,000ha (86 properties) inspected in rabbit-prone areas such as Hawea Flat, Ardgour, Roxburgh and Ettrick, 90% were identified as breaching allowable numbers. Only 11% were fully compliant.
''There are still high levels of non-compliance in historic areas,'' the report said.
In some cases, parts of properties were compliant while other pockets were not.
As a result, the council had requested 79 landowners prepare programmes indicating how they would control rabbits to achieve allowable numbers. So far, 55 had returned a programme.
The council was also supplying more information to landowners to help them develop ''robust'' programmes that were acceptable to the council.
A more proactive approach to encouraging neighbours to develop compatible programmes was also being taken.
