A team of scientists studied 123 sites along 83 kilometres of Upolu's coast in 2016, and their findings have been published in the journal Marine Pollution Bulletin.
In half the sites surveyed, live corals populated less than one percent of a given reef.
At 80 percent of sites, live corals were below 10 percent.
The scientists estimate these reefs may have previously had 60 to 80 percent live coral.
While they say the coral has been buffeted by cyclones and a large tsunami in recent years, much of the damage has been exacerbated by global warming and local pressures.
These local pressures are pollution, land reclamation, nutrient runoff and overfishing, which the authors say should be reined in.
However, coral cover was significant higher in Samoa's marine protected areas, which they say highlights the importance of these reserves to Samoa.