Overfishing and marine pollution are seen as the main reasons for the decline.
60 percent of people in Fiji live in coastal areas and depend on fish as a source of income and food.
Permanent Secretary Sanaila Naqali the Ministry will work with Fijians to implement good fishing techniques.
It has started on projects aiming to ease some of the pressure on the marine life around the reefs, which is a key source of coastal fish.
Mr Naqali said with the projects in place, fish stocks should become sustainable again.