Foreign Ministry spokesman Hong Lei had earlier refused to say whether congratulations would be forthcoming when asked at a regular briefing Monday.
"We noted the decision by the International Olympic Committee," Hong said before referring reporters to the Chinese Olympic Committee, where phones rang unanswered.
Later Monday, the ministry said in an addendum to its transcript of the spokesman's briefing that China's Olympic Committee "had already sent its congratulations to Tokyo for its successful bid to host the Olympics."
It did not say when the congratulations were conveyed.
The Japanese capital's weekend selection to host in 2020 came just days before the first anniversary of the feud that erupted when Japan's government nationalized the islands, called Senkaku by Japan and Diaoyu by Beijing.
Violent anti-Japanese riots erupted in several Chinese cities, and Japanese cars, businesses, and restaurants were smashed and burned a year ago. Beijing issued angry protests and dispatched patrol vessels to confront Japanese ships in the area, sending tensions between the two to a level unseen in years.
Matters have since calmed to the degree that President Xi Jinping held a polite five-minute conversation with Japanese Prime Minister Shinzo Abe at last week's Group of 20 meeting in Russia.
However, Chinese navy ships and air force planes have been operating in international air and waters near the islands in recent days, in what the Japanese government and media have portrayed as unusual amount of activity.
The Communist Party newspaper Global Times offered its congratulations in an otherwise scolding editorial on Monday.
"Although the Sino-Japanese relationship has gone into its worst period in the last 40 years, we still want to offer our congratulations to Japan, and wish the Olympic Games a success," it said.