The season started on April 10 and will run until June 5, despite a Labor-led parliamentary inquiry proposing it be banned from 2024.
Animal Justice MP Georgie Purcell said she was "furious and still in shock" the season was going ahead.
"We're going to see thousands of native birds wounded and left to die out on the wetlands, languishing on their own," she said.
"Birds have to suffer with injuries such as pellets in organs and it can take weeks to slowly succumb to their injuries.
"This is a level of suffering on a scale that is simply unimaginable."
Wildlife Victoria, a statewide animal emergency response service, sent veterinary triage units into wetlands during the opening week.
Chief executive Lisa Palma said there were animal welfare issues related to duck hunting due to the state's unique flora and fauna.
"Wildlife Victoria will need to divert veterinary resources away from hardworking volunteer wildlife rehabilitators ... to provide veterinary care to injured waterbirds illegally left in field,” she said.
"If the government were truly concerned with improving welfare outcomes and hunter behaviour, they would have cancelled the 2024 season and waited until improvements in safety and compliance were made."
An estimated 320,000 ducks were killed in the five-week season last year, according to the Game Management Authority.
BirdLife Australia chief executive Kate Millar said there was concern hunters would be able to request wetlands be reopened if they reported an absence of threatened species at a site.
“The fact that sensitive sites that have protected species will remain open to hunting this season also shows that recreational duck hunting is not a sustainable practice," she said.
The government in January shot down the proposal of a ban, with Outdoor Recreation Minister Steve Dimopoulos describing duck hunting as "a legitimate activity that has existed on these lands for thousands of years".
"It will continue but it has to be safe, sustainable and responsible," he said at the time.
Premier Jacinta Allan denied personal links influenced the decision for duck hunting to continue.
She represents Bendigo East, an electorate with one of the highest number of registered licensed shooters in the state.
Duck hunters will have a bag limit of six per day in the 2024 season.
From 2025, there will be stricter penalties, compliance checks and hunters will have to do mandatory training.
– From AAP.
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