The Japan Football Association (JFA) initially said a bid would hinge on the result of last Friday's International Olympic Committee vote in Copenhagen, won by Rio de Janeiro.
But a JFA official told Reuters on Monday there were no plans to pull out of the running for the 2018 and 2022 tournaments.
Japanese organisers would use venues from the 2002 World Cup, which the country co-hosted with South Korea.
However, new FIFA rules require World Cup host countries build a stadium with a minimum capacity of 80,000 for the opening game and final.
The JFA had planned to use the proposed 100,000-seater waterfront Olympic stadium had Tokyo won the 2016 Olympic vote. Yokohama, venue for the 2002 World Cup final, has Japan's biggest stadium with a capacity of 70,000.
JFA president Motoaki Inukai wants Tokyo - which did not host matches at the 2002 tournament - to stage the World Cup final.
"I want the final to be played in our capital," Inukai told Monday's Japanese media.
The hosts for both 2018 and 2022 will be announced in December next year.
England, Russia, Australia and the United States are among those bidding for 2018 and 2022.
Spain and Portugal have tendered a joint bid, as have the Netherlands and Belgium. South Korea and Qatar have bid for 2022 only.
The 2010 World Cup will be held in South Africa while Brazil will host the 2014 tournament.
