Animal welfare activists will be out in force protesting the start of duck hunting season in Victoria.

Animals Australia and the Victorian government on Friday agreed to halt hunting at Lake Elizabeth in Kerang, which is home to the protected blue-billed duck.

The group will now divert about 150 anti-duck shooting activists, who were going to go to Kerang, to Lake Burrumbeet near Ballarat for the first day of the 12-week hunting season on Saturday.

Animals Australia and the Coalition Against Duck Shooting applied for an urgent injunction in the Victorian Supreme Court to close Lake Elizabeth because of the numbers of blue-billed ducks there.

Wetlands with more than 50 blue-billed ducks are considered for closure as part of measures to protect the threatened species in Victoria.

Both sides appeared in the Supreme Court but activists didn't have to apply for an injunction because the government agreed to restrict access to the site over the weekend.

The state environment department said once it received advice there were 155 blue-billed ducks in the area it acted.

Shooters argue Friday's "shock" decision was based on an outdated counting process and has left hunters disappointed.

So far six Victorian wetlands have been closed for the opening weekend of the hunting season - but there's still around 180 that will be open to shooters.

The state government is yet to decide if Lake Elizabeth should remain closed for the rest of the season.

RSPCA SA and the Animal Justice Party protesters will also gather at Parliament House in Adelaide on Saturday calling for the government to ban the controversial sport.

© AAP 2016