Director General of the Games Toshiro Muto said someone from abroad who is involved in the organisation of the Olympics tested positive.
He declined to say what nationality they were due to privacy concerns, but they were placed in a 14-day quarantine.
It comes after the announcement that the summer's Olympics would go ahead, but without spectators.
Japan's Olympics minister said organisers agreed that fans should not be allowed to attend the games.
Seiko Hashimoto, president of this year's Games, described the situation as "regrettable" and apologised to those who had bought tickets.
Athletes are now beginning to arrive in Tokyo for the Olympics, which will begin on 23 July and end 8 August.