The vessel was one of three that appeared in the waters off the disputed Senkaku Islands, known in China as the Diaoyus, shortly after 9:30 a.m. (0030 GMT) and left Japanese-claimed waters about 70 minutes later, a Japan coastguard spokeswoman said.
The vessel had first been sighted in the area on Tuesday afternoon and was sailing 29 km (18 miles) off one of the contested islands as of 9:00 a.m. (0000 GMT) on Wednesday, according to Japan's coastguard.
At that time, China said its vessels were carrying standard equipment and doing nothing wrong in Chinese waters.
Chinese coastguard vessels sail regularly near the islets but the Japanese coastguard spokeswoman said none had ever been seen equipped with arms.
The dispute over the Japan-controlled islands has been a major sticking point in the two countries' often contentious relations in recent years.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
