The flotilla, noticed by Japan's Maritime Self-Defence Force, sailed between Okinawa Island, the largest in the prefecture, and Miyako Island, the ministry said, as reported by the NHK broadcaster.
The ships were heading from the East China Sea to the Pacific Ocean. The ministry suggested that the vessels took part in some military exercises.
Liaoning ship did not enter the territorial waters of Japan, the ministry added.
This is not the first time Chinese vessels are spotted near Japan. In December 2016, Japan also caught sight of Liaoning passage in the East China Sea. Japan's Defence Ministry was reportedly aware of the passage.