The bid organizers were "highly professional" and preparations were excellent, said International Olympic Committee vice-president Craig Reedie.
"The bid committee has answered our questions sincerely and it was a very impressive effort," he said.
The commission will next tour Madrid and Istanbul, the other two cities vying to host the games.
The host will be selected by secret ballot in Buenos Aires on Sept. 7.
Reedie said the commission witnessed strong government support and growing enthusiasm for the bid.
Prime Minister Shinzo Abe twice met with members of the commission to express his government's backing.
Also, it was announced that public support for the bid had risen to 70 per cent, up from 47 per cent in May. Bid organizers have attributed the increase to Japan's strong showing at the London Olympics where the team won a record 38 medals.
Tokyo, the 1964 host, failed in a bid to host in 2016. Low public support was cited as one of the reasons Tokyo lost out last time, plus its chances were hurt by a demonstration against hosting the Olympics during the commission's visit, but there was no repeat this time.
On recent territorial disputes between Japan and some of its neighbours in the region, Reedie said that was a matter for the IOC members to consider. China and Japan are embroiled in a territorial spat over islands called Senkaku in Japanese and Diaoyu in Chinese. Some have suggested the dispute could hurt Tokyo's chances of landing the games.
"We are aware of the media discussion of those issues," Reedie said. "We have discussed them among ourselves but it was not part of the commission's role. It will be up to each member of the IOC when they come to make up their mind in September."
During the visit, Tokyo organizers highlighted the city's safety and advanced infrastructure, while emphasizing that 28 of the 33 competition venues will be within 5 miles (8 kilometres) of the Olympic Village, which will be built on reclaimed land in Tokyo Bay.