A Chinese navy vessel has aimed a type of radar normally used to aim weapons at a target at a Japanese navy ship in the East China Sea.
Japan's defence minister said the action by China could complicate efforts to cool tension in a territorial row between the rivals.
"Projecting fire control radar is very unusual," Japanese Defence Minister Itsunori Onodera told reporters of the incident, which he said occurred on 30 January.
"One mistake, and the situation would become very dangerous," he said.
Japanese Prime Minister Shinzo Abe, however, told Mr Onodera it was important to respond calmly and not meet provocation with provocation, Kyodo news agency reported.
Mr Onodera said a similar incident may have occurred on 19 January, when a Chinese naval ship may have directed so-called fire control radar at a Japanese navy helicopter.
The long-running row over the islands, known as the Senkaku in Japan and the Diaoyu in China, has in recent months escalated to the point where both sides have scrambled fighter jets while patrol ships shadow each other.
Chinese officials were not available for comment on Japan's complaint about the radar, but a Chinese spokeswoman earlier urged Japan to stop what she called provocation.
"We believe that what is most urgent is for Japan to stop provocative actions like regularly sending in ships and aircraft into the waters around the Diaoyu Islands and seek, via talks with China, an effective way to appropriately control and resolve this issue," Foreign Ministry spokeswoman Hua Chunying said.