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Beijing's apparent snub came after Japan invited representatives from Taiwan to take part on an equal footing with other diplomats in the national remembrance for people killed by the 2011 quake-tsunami.
The move also came as tensions between Tokyo and Beijing simmer over a territorial row, with Chinese government ships on Tuesday spotted in disputed waters, the latest salvo in a spat over the sovereignty of uninhabited, but strategically vital, islands.
"The Japanese government explained to China that we would treat Taiwan appropriately in this ceremony considering its enormous support to us," Chief Cabinet Secretary Yoshihide Suga told reporters.
Tokyo told Beijing "that this would not change Japan's position over the status of Taiwan as stipulated in the Japan-China Joint Communique", he said.
"But China didn't understand and was absent from the ceremony, which is extremely disappointing and a great pity," he said.
China considers Taiwan a part of its territory and aims to bring it back under control, using force if necessary.
In the 1972 joint communique, Japan recognised Beijing "as the sole legal government of China".
Chinese foreign ministry spokeswoman Hua Chunying said on Tuesday that Beijing had made its position known to Tokyo.
"We believe that Japan's behaviour has violated the principles and spirit of the China-Japan Joint Statement and the commitments of the Japanese side," she told reporters.
"We urge Japan to match its words and deeds regarding the issue of Taiwan, to honour its commitment and not play games."
On the first anniversary of the disaster, Japan's then-government, led by Yoshihiko Noda, excluded Taiwan's representative from a list of countries and territories read out at the ceremony.
However, Japan's representative office in Taipei published half-page "thank-you" advertisements in major newspapers on the island, recording the government's gratitude for aid from Taiwan that local media estimated came to $224 million.
Relations between Beijing and Tokyo have deteriorated badly over the last year as the two sides have bickered over the sovereignty of Tokyo-controlled islands in the East China Sea.
Three Chinese government ships spent several hours in the 12-nautical-mile territorial zone off one of the Senkaku islands on Tuesday, Japan's coastguard said in a statement.
Beijing claims the islands under the name Diaoyus. Taiwan also claims them.
Suga said told the press conference that no diplomatic representative from South Korea had been at the tsunami ceremony, in which a minute of silence was observed in commemoration of the almost 19,000 who lost their lives in Japan's worst post-war disaster.
However, he said Seoul informed Tokyo on Monday its envoy's absence was due to a clerical mistake.
Japan and South Korea have a dispute over a different set of islands, which sit in the sea midway between the two nations.