Players had returned to campus for voluntary workouts in Piscataway earlier this month and had been receiving health screenings and temperature checks.
The school says one athlete tested positive in a screening before returning to campus, while the other player tested positive while on school grounds.
"To say we have the answers, that would be an arrogant statement, we are trying to do our best with all the information that we have," Rutgers Football Head Coach Greg Schiano said. "I can tell you that our administration has done whatever we need to do to be able to get this done."
Both players are now under quarantine.
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