The incident on Sunday was the first time that Japan's defence ministry has spotted a live-fire drill by China within its EEZ and disclosed it, Japanese media said.
Relations between Japan and China have worsened since Japanese Prime Minister Sanae Takaichi angered Beijing in November with comments about Taiwan.
The Chinese Luyang III-class missile destroyer was seen conducting the exercise 180 kilometres (110 miles) southwest of the Okinotori island, Japan's southernmost territory.
The move followed an initial sighting around 2:00 am the same day of a fleet of four vessels -- three Chinese ships and one Russian navy frigate -- 330 km southwest of the island as they headed northeast.
When the live-fire training unfolded later, the Russian frigate was also nearby, public broadcaster NHK said.
Following the drill, the defence ministry mobilised a Japanese navy destroyer to surveil and monitor the situation.
Earlier this month, ships from Japan's and China's coast guards faced off near disputed islands, with each claiming they drove out the other's vessels that had intruded into their territorial waters.
The incident took place near uninhabited islands claimed as the Senkaku in Japan and the Diaoyu in China, which sit between Taiwan and Okinawa and have caused diplomatic tensions for decades.