The mishaps have blackened Japan's image as a place that can get things done, a reputation that helped it win hosting rights for the games over Madrid and Istanbul in 2013.
But IOC Vice President John Coates told a news conference after the governing body's fifth review of Tokyo's preparations that everything was going superlatively.
"For a city that's four years out to the Games, I don't think we've ever seen a city more prepared," he said.
"Four years out, we couldn't be happier."
Japan in December selected a stadium design by architect Kengo Kuma to replace original plans dropped last year, an unusual move in response to growing public anger over soaring costs. The decision sparked anger among rugby officials, since the venue had been set to host key matches of the 2019 Rugby World Cup.
Coates said that work on the $1.3 billion stadium would begin in November this year and be completed in November 2019, which he welcomed since this allows time for test events to be held before the Olympics start in 2020.
Kuma said last week that engineers were looking into whether construction could be completed in time to host the 2019 World Cup final.
Coates also said he was pleased with "the level of public engagement" in the selection process for a new Olympics logo and that he looked forward to the final decision, expected in several months.
The original logo was scrapped after plagiarism accusations arose shortly after its July unveiling.
(Reporting by Elaine Lies; editing by Amlan Chakraborty)
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