On Friday, CAS notified Saito he was provisionally banned and had his B sample tested.
According to Martin Rogers of USA Today, Saito's positive test is the first for a Japanese athlete in Winter Olympics history.
According to one report, Seito tested positive for a masking agent and left the Olympic village.
Saito added that, although he wanted to prove his innocence, he did not want to burden his team, which is why he chose to leave, BBC noted.
Russian Federation was barred from this year's games after the International Olympic Committee uncovered a systematic, state-sanctioned doping scheme where agents swapped out about 100 steroid-using athletes' urine samples for clean ones in the dead of night during the 2014 Sochi Olympics.
The athlete was "surprised and dismayed" by the outcome of the drugs test, he said.
Saito had not taken part in any event before the test result from a precompetition sample was confirmed. "I do not want to be a disturbance to my teammates competing at the Olympic Games ... and will leave the team and the athletes village voluntarily".
He was pencilled in as a substitute for the 5,000m on Tuesday.
Yasuo Saito, head of the Japanese delegation, said the skater was "extremely shocked" and "could not comprehend" the test results.
However, it works also as a masking agent that can hide or make it harder for testers to detect the presence of doping products.
Saito denied intentionally doping to CAS, which heard the athlete on Monday.
"So I have no motivation to use this". Acetazolamide, a masking agent and diuretic, is a drug that can not be purchased in Japan without a prescription.
"I want to fight to prove my innocence because I don't remember (taking the drug) and it's incomprehensible", Saito said in a statement after returning a positive test for a banned diuretic.