Salmon remains have recently been found washed ashore on Bruny Island.
Partially rotted salmon carcasses washed up on Conleys Beach on Friday, February 21, followed by balls of fat last week on Tuesday, February 25.
This comes just days after fat balls and salmon oil washed up on Verona Sands beach in the Huon River.
"It is imperative that a full investigation is conducted by the Environment Protection Agency (EPA) Tasmania to assess the biosecurity risk to the entire Huon and Channel estuary, and to identify and fully disclose the company responsible for the pollution, the presence of disease, viruses, bacteria and antibiotics now floating in our public waterways," Neighbours of Fish Farming (NOFF) campaigner Jessica Coughlan said.
Many salmon in southern Tasmania are currently being impacted by a strain of bacteria called RLO, or Rickettsia-like organisms.
RLO does not impact humans or other animals, but is known to be harmful to salmon.
Ocytetracycline is being used to treat affected salmon.
EPA stated that interim laboratory results from the Verona Sands waste do not indicate presence of this antibiotic medicine.
"The public deserves to know how a spill like this could occur under the current regulations, and whether this horrific event constitutes a breach of license conditions, and which penalties will apply," NOFF campaigner Jessica said.
The EPA opened an investigation after the debris washed ashore on Pick Up Beach at Verona Sands.
"Huon Aquaculture Company proactively coordinated initial clean-up efforts around Verona Sands, and the material has been disposed of at an EPA approved facility," EPA said.
"Samples collected by the EPA have been analysed and interim laboratory results indicate the material to be fish oil, likely derived from the elevated fish mortalities that have been affecting multiple pens at Tasmanian fish farms over recent weeks.
"The EPA is monitoring the situation at waste management facilities that it regulates.
"Aquatic biosecurity threats should be reported to Biosecurity Tasmania on 1300 368 550."
Salmon Tasmania, whose three member companies are Huon Aquaculture, Petuna and Tassal, said "We know some of the images being shared are confronting for some people."
"The community can have confidence that the disposal of the fish is being carefully and professionally managed under very strict regulatory conditions.
"It is also important to consider the scale of the losses relative to the size of our industry."