Morais, 29, issued a statement on social media Friday evening.
The Portuguese Olympic team said Morais would not travel to Tokyo as planned.
“I was very careful. I have been fully vaccinated for over a month, but I ended up contracting the virus,” Morais said in a statement issued through Portugal's Olympic team. “I feel fine and I will carry out my isolation. I will be following every second of our team.”
The International Surfing Association had no immediate comment but its deadline to register alternates is Saturday at 3 p.m. Morais is considered to be the best European surfer in the Tokyo Games.
The eight-day shortboard surfing competition period begins Sunday at Tsurigasaki beach.
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