Three operations using baits with either Pindone or 1080 poison are planned by Land Information NZ (LINZ), which administers the Crown land in the two river catchments.
They are part of a range of control measures over seven rivers in the Canterbury region which are administered by Environment Canterbury (ECan).
The only two southern rivers involved in the ground-based operations are the Maerewhenua and Hakataramea rivers.
The control operation in the Maerewhenua is in two stages.
The first, to be carried out between June 11 and July 11, covers 80ha from its river's confluence with the Waitaki River to a site about 30km upstream.
It will use non-toxic baits first followed by green-dyed carrot bait with Pindone poison.
The second site, yet to be scheduled, covers an area from Maerewhenua Rd to Dip Hill Rd, and will use carrots covered with 1080 poison.
The Hakataramea operation, scheduled from June 16 to July 9, covers about 400ha from Hatcheries Rd to Wright's Crossing and will use bait covered with 1080 poison.
The dates depend on weather conditions.
LINZ Crown property manager Bill Naik said the control programme would complement efforts by adjoining landowners to control rabbits in areas where ECan monitoring indicated rabbit numbers were growing rapidly.
"We are pleased with the support we have received from the rural community and Ngai Tahu for this work.
"What we're doing will provide positive socio-economic and land management benefits for farmers and local communities," Mr Naik said.
Most of the work involved ground application of Pindone and 1080 carrot baits on open areas of riverbed frequented by rabbits.
Potential higher use sites were being treated solely with Pindone, and 1080 would not be laid where there was a risk of baits entering water.
"There is no health risk in using areas treated with 1080 or Pindone as long as bait is not handled, children are supervised and animals are not taken from treated areas for eating.
"Consent for each operation is received from the Medical Officer of Health, and independent water quality monitoring is carried out after the treatment," Mr Naik said.
Dogs were highly susceptible to 1080 poison, and owners were strongly advised to keep their dogs away.
Mr Naik urged the public to treat the control areas with caution for six months after the poison was laid, as a precautionary measure.
Adjoining landowners and Te Runanga o Ngai Tahu had been consulted about the work.
Where necessary, further contact was being made with other groups or organisations that may use the areas.
The other sites are on the Clarence, Hapuku, Waiau, Hurunui and Rakaia rivers.