The Northern Territory Government's decision to allow thousands of magpie geese to be caught and sold to restaurants this hunting season has shooters crying foul, after their bag limit was reduced.

The Territory Department of Land Resource Management approved the catching of 4,000 geese this season, which ended Sunday, with the aim of building an export market.

The idea has not gone down well with local hunters who are restricted to shooting for three months of the year and also have to pay for a permit.

NT Field and Game President Bart Irwin said the idea was sprung on hunters, who are perplexed about how the commercial trapping for the purpose of sale had been allowed.

In September, hunters bag limits were dropped from 10 to seven per person amid a drier-than-average wet season and a fall in waterfall nesting.

"I also have concerns about the welfare of birds being trapped and processed," Mr Irwin said.

Mr Irwin said the most recent management program only referred to the possible harvesting of eggs, not the trapping and slaughter of 4,000 live birds.

"It's fraught with danger," he said.

"Would you start an industry in dugong or crocodile harvesting from the wild?

"It shouldn't go ahead and I'll be discussing it further with the department."

Mr Irwin said it was also likely a black market in magpie geese could see hunters trying to sell their catch directly to restaurants.

"Certainly restaurants can buy 20 birds a week, they'll say yeah that's what we'll serve and they'll buy those through the front door with the certified seller and through the back door will come another 200 birds at a lot cheaper rate and there is no way that can be policed," he said.\