Saito, 21, failed an out-of-competition test prior to the event, the anti-doping authority said in a statement, adding that he tested positive for acetalozamide, a banned diuretic which is considered a masking agent.
The CAS statement said Saito had left the athletes' Olympic Village voluntarily and would be provisionally suspended from the Olympics and other competitions pending a full investigation.
Saito, a human biology student whose sister Hitomi is also competing in Pyeongchang, becomes the first Japanese athlete to test positive for doping at a Winter Olympics, according to Japanese reports.
Saito was a member of Japan's 3,000m relay team that finished third at the 2013 and 2014 world junior championships.
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He competed on Saturday in the short track speed skating 1,500 metres but was eliminated in the heats.
He was pencilled in as a substitute for the 5,000m on Tuesday.
Saito was summoned before the CAS tribunal on Monday following the positive test for acetalozamide, a medication used to treat complaints ranging from epilepsy to heart failure.
The IOC and anti-doping authorities have stepped up testing for the Pyeongchang Games following revelations of a state-sponsored doping scheme at the last Winter Olympics in Sochi, Russia, in 2014.
The entire Russian team was banned from Pyeongchang but a loophole allowed 168 "clean" athletes to compete as independent athletes under a neutral flag.