Kendricks, the reigning world champion, has been ruled out of the Games.
The Australian Olympic Committee said in a statement that athletes are isolating in their rooms as a “precautionary measure” and are undergoing testing procedures.
The athletics starts on Friday.
Kendricks, 28, won Olympic bronze in Rio five years ago and had been expected to contend for a medal in Tokyo.
He won the world pole vault title in 2017 and 2019.
“In alignment with local rules and protocols, he has been transferred to a hotel to be placed in isolation,” the United States Olympic and Paralympic Committee (USOPC) said.
“Sam is an incredible and accomplished member of Team USA and his presence will be missed. Out of respect for his privacy, we cannot provide more information at this time.”
Kendricks’ father Scott, who is also his coach, said on social media his son is not experiencing symptoms.
Argentine pole vaulter German Chiaraviglio has also tested positive for Covid-19 and been ruled out of the Olympics.
On Thursday, the International Olympic Committee said two Olympic-related Covid-19 cases are being treated in hospital, although not in intensive care.
There have now been 193 cases among Olympic personnel, including 20 athletes.
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