Australian media reported that all 63 members of the team were in isolation after pole vaulter Kurtis Marschall had been training with Kendricks.
Games procedures state that athletes who are contact-traced and have not yet competed are isolated from the rest of the squad. They then have to be tested six hours prior to their competition and return a negative result in order to compete.
The athletics programme begins on Friday, with the pole vault qualifying event on Saturday.
“Members of the Australian track and field team are now undergoing testing procedures in line with Australian Olympic team protocols,” the Australian Olympic Committee (AOC) said in a statement on Thursday.
Kendricks’ dad posted on social media that his son had no Covid-19 symptoms, but was informed while in Tokyo that he tested positive and was out of the competition.
The US Olympic and Paralympic Committee confirmed the news and said Kendricks has been placed in isolation at a hotel.
Kendricks, who holds the US record, is being supported by the USOPC and USA Track and Field.
Kendricks won the world title in 2017 and 2019 and Olympic bronze in Rio 2016, and his battle with world record holder Mondo Duplantis of Sweden was expected to have been one of the highlights of the track and field programme.
Additional reporting by AP.