Wildlife enthusiasts and environmentalists are critical of the farms' position, reports broadcaster NRK.
The conflict is between salmon farmers, who had around 780 million fish in their facilities in 2016, and close to 20,000 pairs of great cormorants that nest along Norway's coast, according Artsdatabanken figures.
Holding companies owning the farms have been granted permission to shoot cormorants who catch their fish in both the Åfjord and Vikna areas of Trøndelag county, reports NRK.
The Norwegian Ornithological Society and Norwegian Society for the Conservation of Nature (Naturvernforbundet) have both called the decision an error and appealed against it, according to the report.
"It is sad and a little meaningless that an industry that already has a considerable problem with its reputation, including stray salmon, salmon lice and death of shrimp populations is now also shooting sea birds," Norwegian Ornithological Society general secretary Kjetil Ådne Solbakken told NRK.
The farms should be responsible for keeping the birds away from their facilities and coexisting with natural habitats, rather than destroying them, he said.
Salmon farming company Midt-Norsk Havbruk is one of the firms that has been granted the licence to shoot cormorants.
Head of production with the company Frank Øren said it would only be made use of when highly necessary.
"The cormorant can get stuck in nets, or problem animals that cannot be scared away can come. So we want to have the necessary permissions," Øren said to NRK.
Martin Eggen, an advisor for wildlife protection groups, disputed that statement.
"The law says that farms should do everything they can to prevent conflicts while documenting large economic losses, but the applications that are now being sent to municipalities are extremely superficial," he told the broadcaster.
Solbakken rejected industry claims that cormorant populations have increased, citing new figures from the Norwegian Institute for Nature Research.
"Over half of the cormorants that nest along Norway's coast have disappeared in a short space of time," he said.
He also criticised the industry for looking to expand into protected areas.
"In the Froan island group in Trøndelag we saw, for example, that protection of a large area was lifted as a concession to salmon farming. So when an industry with these views expands so much, it's worrying," he said.
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