The case discovered on Thursday involves a Games-related member of staff who is not resident in Japan, according to organisers, who did not give further details.
There have not yet been infections reported among athletes in the village, which opened to Paralympians on Tuesday.
The Games will see about 4,400 athletes from 160 teams compete in Tokyo from August 24 to September 5.
Those staying at the village will be required to undergo daily COVID-19 testing, wear face masks and maintain social distancing, as was the case during the Olympic Games, which ended on August 8.
The Paralympics begin around two weeks after the Olympics ended, with organisers saying they were able to prevent any major spread of infection through tough anti-virus measures.
So far, 546 positive cases linked to the Olympics have been reported, and some experts have argued that holding the Games undermined the government’s messaging on virus rules and contributed to a surge in domestic infections.
In recent days, Japan has recorded more than 20,000 daily virus cases, more than ever before, and the government has expanded and extended virus states of emergency to cover 13 regions until September 12.
The measure largely shortens restaurant and bar opening hours and bans them from selling alcohol, but experts have questioned the efficacy of the restrictions with cases continuing to rise.