The Great Barrier Marine Park Authority (GBRMPA) does not test cobalt according to its current water quality.
Green turtles are vulnerable to Australian waters, but the International Conservation Union is at risk.
Researchers believe that green turtles may be equivalent to a canaryman in a coal mine, giving an early warning to chemical release to the Great Barrier Reef system.
The WWF Australian Maritime Nature Project Manager Christine Anne Madden Hof noted that cobalt was found in areas that could also cause "toxicity in other species".
"We believe that metals found in turtles are washed away from natural and human sources," Madden Hof said.
"The relationship between cobalt and cobalt in turtles is consistent with the theory that Upstart Bay had acute cobalt exposure in 2012."
23 percent of green turtles in Upstart Bay and 10 percent of green turtles were found in Cleveland Bay nearby.
"The current reef control programs do not test many pollutants detected by our projects, which is why we require checks on a broad range of chemicals, including metals," Madden Hof said.
"If we find all these impurities in just two coastal areas, what's happening in the other bays and estuaries in the reefs?
"We have shown that turtles are good indicators of reef health because they absorb chemicals in their environment.
"The methods developed for this project can provide a cost-effective, early warning sign for poor water quality and chemical contamination."
Changes in water quality testing were considered, the GBRMPA spokesman confirmed.
"With Marine Park Authority's marine monitoring program we are testing sediments, nutrients and pesticides," he said, "for water quality, these are the greatest risk to the reef."
"We are currently developing the integrated monitoring and reporting program of the Reef 2050, which includes the primary tracking indicators as well as the measurement methods, locations and frequency of the indicators."
This new test program will be finalized by 2019.
A large number of experts have been involved in advising on prioritizing and selecting the indicator.
Protective Turtles are currently the National Recovery Plan for the Australian Sea Turtles, the regionally focused Reef 2050's Long-term Sustainable Development Plan and the Queensland Sea Turtle Conservation Strategy.
"We support independent research and, like all relevant studies, the WWF report is considered as part of our normal computing processes and their current management plans," the spokeswoman said.
Tony Moore is a senior reporter from Brisbane Times