Chinese Vice-Premier Wu Yi cut short a visit to Japan and cancelled talks with Prime Minister Junichiro Koizumi which had been aimed at easing troubled ties.
Wu Yi acknowledges ties with Japan are currently difficult
Beijing cited unspecified "domestic duties" for the cancellation, but a top official of Japan's ruling party said the move could be seen as "rude".
China and Japan's ties have been dogged by rows over Tokyo's attitude to its war-time history and other disputes.
Last month, anti-Japan demonstrations took place in several Chinese cities.
Ms Wu, who arrived in Japan last week, was expected to meet Mr Koizumi on Monday, but cancelled the meeting and left the country a day ahead of schedule.
She did, however, keep an appointment to have lunch with Hiroshi Okuda, the head of Japan's largest business lobby, Keidanren. China is Japan's biggest trading partner.
Mr Koizumi said he did not understand why their meeting had been cancelled, saying it was Beijing that had requested it in the first place.
"I would meet with them anytime," he said.
Ms Wu's early departure came one day after Chinese President Hu Jintao told members of Japan's ruling party, visiting Beijing, that they should stop going to Japan's Yasukuni war shrine.
The shrine is dedicated to the souls of those Japanese who died in wartime, including some convicted World War II criminals, and is viewed by China as a symbol of Japan's past militarism.
Mr Koizumi is a regular visitor to the shrine. On Friday he defended his visits before the Japanese parliament, arguing that he undertook them as a private individual, rather than as prime minister.
Tokyo said there was no link between Ms Wu's change of plan and Beijing's views on the shrine.
"The Chinese side made it very specific that it has nothing to do with Yasukuni," said Japanese Foreign Ministry deputy spokesman Akira Chiba.
An official in Mr Koizumi's Liberal Democratic Party warned, however, that some people in Japan might regard it as a snub.
"If it is due to urgent business it can't be helped, but many people in Japan may feel it is rude," said Shinzo Abe.