The head of Tasmania’s EPA has defended his use of Tassal’s own data to approve the company’s new waste system.

EPA director Wes Ford notified the media of his decision to approve salmon farmer Tassal's faecal capture system at 5:30pm last Friday, a time usually picked for its lack of media attention.

Tassal was told earlier this year that it had to set up a system under some of its pens to stop the waste from its 6,000 tonnes of fish from spreading too far.

Tassal put up plans to surround the bottom of its giant fish cages with a tarpaulin funnel, which forces waste down into a pump tube, where it is pulled back up onto a nearby boat.

The EPA has approved the company’s plans, and Mr Ford says the approval was given without an independent scientific assessment because he “witnessed firsthand the extraction of the waste from one of the liners and the removal of it”.

“I was satisfied the waste collection system [was] going to work,” he told ABC Radio.

“Why would I have it independently assessed? I value my own judgements.”

Rival salmon producer Huon Aquaculture says the approval shows the EPA’s favouritism towards Tassal.

Huon recently launched legal action against the Tasmanian Government and EPA for allegedly failed to protect Macquarie Harbour, kicking off a fight in which Tassal has sided with the Government.

Tassal is planning to expand its operations on Tasmania’s east coast, but conservationists say the ecosystem cannot handle it.

Meanwhile, Mr Ford says it will be months before the effects of the new waste collection system will be known.