Protests over the Senkaku Islands -- called Diaoyu Islands in China -- occurred as demonstrators also marked the anniversary of the 1931 invasion of China by Japan, Kyodo News reported.
The latest developments came as U.S. Defense Secretary Leon Panetta arrived in Beijing for a three-day visit, which is to include defense talks with Chinese military officials.
The islands, which aren't inhabited but are believed to be rich in natural resources, are claimed both by China and Japan. China's claims have intensified since last week when Japan, which controls the islands, announced it would put them under state control. Taiwan also has a claim on the islands.
The issue has become tense with China sending surveillance ships to the island waters, which Japan says are its territorial waters.
In Beijing, Kyodo reported about 1,000 people demonstrated at the Japanese Embassy. Similar rallies were reported near Japanese diplomatic missions in Shanghai, Guangzhou in Guangdong province and Shenyang in Liaoning province, Kyodo said.
"China will never forget Sept. 18, 1931, because it was the beginning of the darkest period in China's modern history," the China Daily said in an editorial. It was in reference to the invasion by Japan after the Mukden incident when a portion of the Japanese railroad in Manchuria was blown up, which the Japanese military blamed on Chinese dissidents.
Separately Tuesday, Chinese media were quoted as saying about 1,000 Chinese fishing boats were expected near the disputed islands in the next few days to protest Japan's nationalization.
Kyodo said if such a large number of Chinese vessels enter Japanese territorial waters, it could trigger incidents with Japanese coast guard patrol ships.
While in Japan, Panetta repeated the U.S. position on the islands dispute, urging Japan and China to peacefully resolve the territorial issue.