The annual football tournament, at which the champions from the six global confederations compete along with the host nation's top team, was due to be held there in December.
"We had to make a decision at this time," JFA Secretary-General and CEO Kiyotaka Suhara told a press conference.
The Club World Cup was last held in Japan in 2016, and the JFA had planned to host the 2021 edition as part of its 100th-anniversary celebrations.
The tournament usually takes place in December, but the 2020 edition in Qatar was postponed to February 2021 because of the Covid-19 pandemic, with Bayern Munich the winners.
Japan has battled a record fifth wave of virus cases driven by the more infectious Delta variant this summer, even as the Tokyo Olympics and Paralympics went ahead under strict virus restrictions.
Much of the country is currently under anti-infection measures that limit the number of spectators at sports events.