The Victorian government announced on Tuesday it was permanently introducing a kangaroo harvesting program after having undertaken trials for five years.

Commercial quotas for seven areas across the state have been set for October to December.

In the North East, a mark of 2945 kangaroos has been nominated, the second highest in the state behind the Lower Wimmera on 4115.

The North East extends from Greater Bendigo and Campaspe council areas through to Towong and south to Mansfield Shire.

Another quota will be set for 2020 and further tallies will be prescribed annually.

Agriculture Minister Jaclyn Symes said the measure would help farmers.

"The program balances the need to keep kangaroo populations at healthy levels and ensure farmers aren't being overrun by roos who can eat crops, damage property, and compete with stock for feed and water," Ms Symes said.

Nationals Victorian leader and Opposition agriculture spokesman Peter Walsh has questioned why the permanent program will not allow kangaroos killed with an authority to control wildlife permit to be processed.

"It's absurd that kangaroos controlled under an authority to control wildlife permit will now be left in the paddock to rot, feeding up wild dogs and foxes," Mr Walsh said.

"After the Andrews Labor Government's lacklustre approach to this program over the past five years, it remains to be seen if the latest changes will work or if processors, hunters and farmers are just being wrapped up in more red tape."

Under the regulations for the scheme, kangaroo shooters will be required to be authorised and trained.

Harvesters are being advised to ensure their vehicles, equipment, clothing and footwear are free of contaminants and disinfected away from crops and livestock.

Landholders wanting to engage harvesters are required to provide written approval to an authorised shooter.

They are also urged to seek evidence that the harvester is covered by public liability or indemnity insurance.