In August, the inquiry called for recreational duck hunting to be banned across all Victorian public and private land from 2024.
But the government shot the proposal down after Premier Jacinta Allan and ministers met on Monday to thrash out a response.
The season will run from April 10 to June 5 with a bag limit of six per day.
"This is a legitimate activity that has existed on these lands for thousands of years and at least, in terms of white Australia, from 1860," Outdoor Recreation Minister Steve Dimopoulos said.
"It will continue but it has to be safe, sustainable and responsible."
From 2025 there will be stricter penalties, compliance checks and hunters will have to do mandatory training.
The details are yet to be worked out but Mr Dimopoulos said they would cover marksmanship to improve animal welfare outcomes and Aboriginal cultural heritage awareness, with the program to be developed with wildlife and hunting groups.
"Sitting in front of a computer won't cut it, you can't be a better marksman and actually be able to cause less suffering from an animal just by (sitting at) a computer," he said.
Steve Dimopoulos says duck hunting will continue but has to be safe, sustainable and responsible. (Joel Carrett/AAP PHOTOS)
Duck hunting has long been banned in Western Australia, NSW and Queensland but is still legal in Victoria, South Australia and Tasmania.
Mr Dimopoulos said the government would implement seven of the inquiry's eight recommendations to overhaul hunting but a total ban was not necessarily needed to make the practice sustainable and safe.
RSPCA Victoria chief executive Liz Walker said allowing duck and quail hunting to continue would fly in the face of the inquiry's recommendations, the government's progress on animal welfare reforms, the clear evidence of its harms and public sentiment.
"We urge the government to hear the millions of Victorians who have made clear their support for a duck hunting ban in Victoria and to reverse this decision," Dr Walker said in a statement.
Animal Justice Party MP Georgie Purcell, who was on the nine-member select committee, said the government had treated native waterbirds with disdain and she would no longer help it in the upper house.
"It is gutless, it is spineless and it is completely unforgivable," she said in a statement.
"They have made a mockery of parliamentary processes to appease the personal interests of a few, rather than the majority of Victorians."
Georgie Purcell has been a long-term opponent of duck hunting. (Diego Fedele/AAP PHOTOS)
Danny Ryan from the Victorian Duck Hunters Association, on the other hand, welcomed the decision.
"Good government considers outcomes for all Victorians, not just a very small minority of animal activists," the former Field & Game Australia chairman told AAP.
"Hunting groups and organisations are committed and ready to work with government to assess and implement those changes."
Despite there being no definitive evidence on wounding rates, the committee found thousands of birds were wounded each year and described it as an "unacceptable animal welfare outcome".
In June, Electrical Trades Union state secretary Troy Gray told the committee any duck hunting ban would trigger a mass walk-off on projects across the state.Â
Shooters, Fishers and Farmers MP Jeff Bourman told reporters he was relieved and hunting only remained legal due to help from unions and some Labor MPs.
"For a long time there I thought we were done," he said on Monday.
Opposition Leader John Pesutto said the government had wasted a lot of parliamentary time commissioning an inquiry and then ignoring its findings.
"There's no direction under Jacinta Allan. What we're seeing is a government that makes it up as it goes along," he said.
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