Labor has renewed discussion over the divisive issue after its plan to bring back an independent watchdog to oversee the live export regulator was debated in federal parliament on Monday.

"Ninety-nine-point-seven cent of sheep that go to live export go off the ship in a better or same condition," Mr Joyce told the lower house.

Shutting down the industry wasn't the answer to solving issues, he added.

Labor MP Meryl Swanson questioned Mr Joyce's statistic, but said the treatment of the remaining animals had troubled many Australians.

She had received thousands of emails on the issue, she said.

"We have to treat those animals with respect, and I think that's why we've seen such a heartfelt response from Australians."

Labor appointed an interim independent inspector-general in 2013 but lost government before the position could be cemented.

Opposition agriculture spokesman Joel Fitzgibbon introduced a private member's bill in June to reinstate the role, in response to scandals in the sector sparked by video footage showing sheep dying in horrific conditions onboard a Middle-East bound ship.

Mr Joyce fears shutting down the live export industry would hurt Australia's relationship with the Middle East.

"They might have a parochial approach to how they trade with us, or whether they do at all," he said.

The coalition government has stalled legislation for tough new penalties for dodgy exporters, after Labor tacked on an amendment which would shut the industry down over five years.

Nationals MP Michelle Landry urged Labor to back improvements to the industry, rather than trying to shut it down entirely.

Australian Associated Press