Japan Football Association (JFA) vice president Junji Ogura said last month any bid would depend on Tokyo winning the vote for the 2016 Olympic Games.
The country does not currently have an 80,000-capacity stadium required by FIFA and organisers had planned to use Tokyo's proposed 100,000-capacity Olympic stadium plus venues from the 2002 World Cup, which the country co-hosted with South Korea, for the 2018 or 2022 tournaments.
"Even if (Tokyo's bid) fails it does not mean we will automatically pull out (of the World Cup bidding)," Inukai told reporters on Monday. "We will examine the possibility of hosting the World Cup independently."
The JFA told Reuters on Tuesday there was no confusion or difference of opinion between the association's top two officials despite the apparent U-turn made by Inukai.
