The authority said ISA was detected on the company's farm in Chiloé, during an audit conducted last January.
Invertec has twice gone to court so that it would not have to harvest infected cages, which in the opinion of the fisheries authority, "threatens the entire industry".
Two-star Global Aquaculture Alliance Best Aquaculture Practices (BAP) shrimp standards are now equivalent to a yellow “Good Alternative” rating from the Monterey Bay Aquarium Seafood Watch programme.
The determination came after an extensive evaluation of BAP farm standards for finfish and crustaceans conducted by the Seafood Watch science staff.
The process of benchmarking existing eco-certification programs against Seafood Watch criteria began more than two years ago when Seafood Watch business partners sought guidance in navigating a marketplace of proliferating global eco-certification programmes.
“This is a landmark recognition for the BAP certification programme,” said Peter Redmond, BAP vice president of market development.
“We have strived for years to deliver high-quality seafood to the marketplace that is farmed in a responsible way.”
Peru requires an investment of $118 million into research and development to reduce the gap in aquaculture and to achieve the level of other countries such as Chile, reported Andina.
"We have to take a big leap, we have to think big and we need the $118 million to boost aquaculture," said the deputy fisheries minister, Paul Phumpiu.