Huon Aquaculture Company will have to pay more than a quarter of a million dollars for an environmental study after it exceeded a farming licence condition regarding nitrogen levels.

The company, one of Tasmania's biggest farmed salmon producers, reported to the Environment Department (DPIPWE) that it had exceeded its forecast levels of nitrogen input into the Huon River and Port Esperance area by 277 tonnes or 42 per cent over 12 months.

Salmonid marine farming operations in the Huon River and Port Esperance Marine Farming Development Plan 2002 are subject to an upper limit on the amount of dissolved nitrogen that can be released into the plan area.

The company has been ordered to pay the full $260,000 cost of a comprehensive assessment to determine the extent of any environmental consequences, and this has been reflected in amended marine farming licence conditions.

DPIPWE has asked the Institute of Marine and Antarctic Science (IMAS) to make the assessment.

The assessment will cover key questions in relation to the exceeded dissolved nitrogen levels, including the timing, nature and location of the elevated levels, and any effects.

Huon Aquaculture blames additional feeding

The company said it alerted DPIPWE to the situation, blaming additional feeding.

Huon Aquaculture's Peter Bender said the extra feeding was temporary and he believed there would be no impact on the area.

"All of our monitoring to date has given us no cause for concern for the health of the waterway in and around our leases," he said.

"We believe this is largely the result of the work we have done to site leases further offshore and into better mixed and flushed waters in the overall system.

"That said, we also welcome the State Government’s independent scientific study that will be undertaken by IMAS and we look forward to seeing the results of the research."

Mr Bender said the growth rates in the salmon had been unprecedented, which he attributed to new pens and feed technology.

"The performance of the new Fortress Pens and feed technology has been astounding, and we've experienced our strongest growing season on record, which on the one hand is terrific, but on the other hand meant we were feeding bigger fish more feed," he said.

"The success of the changes made through the Company’s Controlled Growth Strategy have taken us by surprise."

Mr Bender also said unforeseen delays in changes to leases, and the move to offshore farming in Storm Bay had also played role.