Hundreds of passengers joined Japanese sports stars of past Olympic and Paralympic Games and young athletes to mark the milestone.
Among those in attendance was retired weightlifter Yoshinobu Miyake, who won under 60 kilograms gold at the Tokyo 1964 and Mexico City 1968 Olympic Games.
"It is an honour to be a part of this celebration today," he said.
"It brings back so many memories of the 1964 Olympic Games.
"The Tokyo 1964 Games showed how sports could change the world and our future, and I am confident to say the same today.
"I am thrilled to see that Tokyo 2020 Games will become another unforgettable page of our history and bring many more positive changes in our country."
During the event, children and adults made 2,020 origami cranes with wishes and hopes for the Tokyo 2020 Games.
Children from Tokyo’s Ōta ward put the finishing touches to the cranes, which were used to complete a monument, in the shape of the globe, highlighting the next two Summer Olympic host cities of Rio de Janeiro and Tokyo.
"I hope that Tokyo 2020 Games will inspire you to practice sports, achieve your personal best and share your passion with others," rifle shooter Yui Ueda, who was representing the next generation of athletes, told the school children.
"We are the future of Japan and Tokyo 2020 are our Games."
Aki Taguchi, who competed for Japan in shooting events at the Athens 2004, Beijing 2008 and London 2012 Paralympic Games, was also present.
"I believe that Tokyo 2020 will set a new benchmark for the Paralympic Games," she said.
"Tokyo 2020 will offer the world-leading accessible infrastructure, but also bringing in new perspective to people’s mind and an unprecedented atmosphere of equality and unity in diversity through the Games.
"I hope that these positive changes will be connected to future and become a new legacy beyond 2020."
Earlier this month, Hiroya Masuda, a candidate to be the next Governor of Tokyo, vowed to "speed up" Tokyo's preparations for the 2020 Olympic and Paralympic Games.
A number of Japanese politicians and officials have put themselves forward for the position, vacated last month by Yoichi Masuzoe, who resigned after he was accused of misusing public funds.
The successful candidate will become the third Tokyo Governor since the city was awarded the 2020 Olympics and Paralympics in 2013.
One of their first official duties will be to accept the Olympic flag from Brazilian organisers as the head of the next host city at the Closing Ceremony of Rio 2016 on August 21.
This was expected to be performed by a temporary Governor but the new leader of Tokyo is now likely to take over, with the vote scheduled for July 31.
Masuda, a former bureaucrat backed by Prime Minister Shinzō Abe's ruling Liberal Democratic Party, will go up against Yuriko Koike, Japan’s first female Defence Minister, and a host of others in the race to become Masuzoe’s successor.
Tokyo has already faced many problems with its bid, with the original logo scrapped due to a plagiarism row and the initial Olympic Stadium design shelved thanks to spiralling costs.
These were followed by allegations of a suspicious payment made by Tokyo 2020 to Black Tidings, a Singapore-based firm with links to the son of former International Olympic Committee member Lamine Diack, during its successful bid campaign.
Black Tidings is already under investigation by French prosecutors as part of an inquiry into its use to channel money involved in the cover-up of Russian doping cases.
Japanese Olympic Committee President and Tokyo bid leader Tsunekazu Takeda insists the fee was for legitimate consultancy work, but a probe is continuing.