The talks involving a high-ranking official from the Chinese foreign ministry's Asian division were thought to have been held in early October, Japanese news agency Jiji Press reported from Beijing quoting Chinese government sources.
A high-ranking official from the Japanese foreign ministry attended the meeting, the report said.
A Japanese foreign ministry official declined comment on the content of the report, saying: "Japan and China have been making various exchanges at various levels."
The row over the islands in the East China Sea has led to warnings of a possible armed confrontation.
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Japanese Prime Minister Shinzo Abe managed a brief encounter and shook the hand of Chinese President Xi Jinping last week on the sidelines of an Asia-Pacific summit in Indonesia. But China rejected a formal sit-down meeting between them due to the island dispute.
Abe has not held formal talks with Chinese and South Korean leaders since taking office last December. Tokyo also has a dispute with Seoul over a group of South Korea-controlled isles.