Japan claims a Chinese frigate has directed radar used to launch weapons at one of its destroyers in waters near islands which both countries claim as their own.
If true the incident marks a new level of danger which analysts fear could one day lead to a war between Japan and China.
The Japanese Defence Ministry says a "fire-control radar" was directed at their ship on January 30, and disclosed that a radar was aimed at a Japanese helicopter on 11 days earlier.
On both occasions the location was in the East China Sea, near the islands known as the Senkaku in Japan and Diaoyu in China.
The islands are uninhabited but controlled by Japan.
This is the latest incident in a series which has significantly raised the temperature in the region after Japan said it would buy several of the islands from a private owner last summer.
The Chinese sent in paramilitary ships which were intercepted by the Japanese coast guard and then followed up with a "civilian" flotilla sailing to the islands.
This caused the US to send a diplomatic team to Japan to urge caution on both sides.
Instead, the opposite has happened. Three of the islands were purchased last September triggering a wave of anti-Japanese rioting in China.
The Chinese now send surveillance aircraft near the islands which on at least one occasion has caused the Japanese to scramble fighter jets.
The US is concerned because its treaty obligations, depending on how they are interpreted, could mean they would have to intervene militarily on the side of the Japan if a war broke out.
It is doubtful that either side wants war, but the Japanese have a newly elected nationalist government, and China is increasingly pushing out with a more aggressive foreign policy.
That volatile combination has set nerves rattling.