The certification will apply to marine fish farms that prove they are free from the use of antimicrobials and antiparasitic treatments throughout the production cycle.
Alicia Gallardo, Deputy Director of Aquaculture Sernapesca, explained that this certification has been developed due to the interest of companies in demonstrating that that they have not used these types of medication.
"We hope that with this certification companies will be motivated to avoid the use of these treatments during the production cycle," Ms Gallardo said.
The first two centres to be accredited belong to Nova Austral and are located in Magallanes region.
In other news, Japan's Nippon Suisan Kaisha Ltd. is to begin selling bluefin tuna which has been farmed from egg to adulthood.
The Japan Times newspaper reported that sales of the fully farmed tuna will begin in winter 2017.
The company expects to ship 10,000 tuna (500 tons) in the fiscal year starting April 2018 and double that in the following year.
The tuna will be sold to restaurants, supermarkets and other retailers, company officials said.