The city hosted the summer games in 1964 and its new bid was welcomed by the Japanese Olympic Committee (JOC).
"We would like Tokyo to do their best to produce a wonderful plan," said JOC chairman Tsunekazu Takeda.
Tokyo entered the race after two other cities, Sapporo and Nagoya, ruled themselves out.
Sapporo, which hosted the 1972 Winter Olympics, said it would be unable to raise the estimated $2.1bn needed to cover its share of the £15.2bn total cost of the Games.
The JOC will select the country's official bid city in August while the International Olympic Committee will decide who stages the 2016 Games in 2009.
