According to ABC, head of Pork Queensland, John Coward, said the increase in licence fees over the past few years and a hike in the cost of feed have seen profit margins collapse.

Fees have risen for bigger farms that produce more waste and present a higher environmental risk, but some farmers aren't coping.

For the past 30 years, Greg Upton has run a piggery at Murgon and said he'll be shut down if he can't raise the funds for his licence.

Under the Environmental Protection Act, his licence fee is just over $3,000, which he said has risen $400 in the past five years.

He's classified as a bigger farmer because he has approval for 2,000 SPUs - that's standard pig units - but he said he only runs a fraction of that because he can't afford to expand.

He said he can barely scrape together this year's fee.

"We will actually borrow the money. We had $20,000 in farm bonds, we brought that back into the business, my wife, she's just cashing in an insurance policy now, our overdraft has gone to the hilt."

Piggery operators can apply for a fee reduction of up to 20 per cent if they can prove they have a certain environmental management system or a lower emissions score.

But Mr Upton said it would cost him more to get a discount than what the discount would actually be worth.

He said other operators have been shut down, and he's worried he'll be next.

"They've already shut down, I think, a person in Toowoomba ... my neighbour, he has a piggery, he refused to pay it, and he was going to be deregistered," he said.

"It's certainly not democracy in this country any more."

Pork Queensland's John Coward said problematic fee structures, as well as the crippling drought, mean Queensland farmers are worse off than others across Australia.

But he's working on getting government backing to relieve the burden.

"One of the things we'd like to see is a more equitable spread of fees across the whole production range, so that a person that has got say 10 pigs more than the lower limits doesn't automatically jump up to a higher limit."

He said the government is considering the request, and has taken a more philosophic approach to the costs of pig production.

The Department of Environment and Heritage Protection refused an interview, but did provide a statement outlining details of the licence fee.