The rules allowed wombats to be controlled for specific purposes without the need for a permit in a small part of the state's east.

Animal welfare advocates welcomed the move, which comes after a state government probe into reports of the animal being hunted for sport.

Landowners in the Gippsland region, where the wombats have been considered 'unprotected', will now need to apply for a permit if they want to kill the animals.

Victorian Environment Minister Lily D'Ambrosio said on Thursday that the previous rules were outdated.

"Wombats deserve the same protection as other native animals - and that's what this change delivers," she said.

"This change will ensure wombats can't be exploited by an old rule."

Anyone caught killing wombats without authorisation could face a fines up to $39,000 and a maximum of two years in jail under the Wildlife Act 1975 which makes it an offence to kill, take, control or harm native wildlife.

The change - which takes effect on Thursday - comes after reports of "wombat hunting" tourism where people travelled to regional Victoria to hunt the animal for sport.

The reports prompted Ms D'Ambrosio to order an inquiry in August, which delivered its findings in late 2019.

Animal group Humane Society International said the rule change will close a "dreadful chapter" in Victoria's history.

"For decades the atrocious loophole has given landholders across much of eastern Victoria free reign to cull wombats on their land," the organisation's Head of Programs Evan Quartermain said.

"A lack of oversight means the scale of suffering this 'unprotected' status has caused is largely unknown, but our analysis suggests it likely resulted in tens of thousands of wombats being shot with impunity."

Mr Quartermain said the state government should now turn its attention to curbing the number of wombat deaths being authorised, which he put at more than 25,000 in the past decade.

"With simple solutions to prevent wombat damage to properties such as wombat gates now available there is simply no excuse for the carnage to continue," he said.

Victorian Greens MP Sam Hibbins also stressed the number of wombats being killed is too high.

"The killing of wombats is out of control in Victoria ... a non-lethal and humane approach to dealing with wombats must be enforced," he said.

Australian Associated Press