The person who tested positive for the virus is not an athlete and is not a resident of Japan, they added.
Organisers have already reported more than 70 Covid cases linked to the Paralympics, mostly among contractors and staff.
The Games are due to begin in five days on 24 August.
Around 4,400 athletes from approximately 160 teams are set to take part in the Paralympics.
As with the Olympics, they will be required to undergo daily Covid tests, and will have to wear face masks and maintain social distancing within the Paralympic village.
Tokyo is currently under a fourth state of emergency, and organisers have decided not to allow any spectators during the Paralympics.
Organisers say they managed to largely keep Covid at bay during the Olympic Games earlier this month through tough anti-virus measures.
However, critics say the Games contributed to a surge in infections within the country.
In recent days, the Japanese capital has reported more than 20,000 cases per day, more than ever before.
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