Abe has in the past been critical of China's assertiveness in the South China Sea, through which much of Japan and South Korea's trade and energy supplies pass.
"He said Japan would like to cooperate with South Korea and the United States at various occasions to preserve the open, free and peaceful sea," Deputy Chief Cabinet Secretary Koichi Hagiuda told reporters in a media briefing after Abe held talks with President Park Geun-hye of South Korea in Seoul.
Hagiuda did not elaborate, but on Friday, Japanese Defence Minister Gen Nakatani reiterated that Tokyo had no plan to take part in US-led "freedom of navigation patrols" in the South China Sea.
A US warship sailed within 12 nautical miles of one of China's man-made islands in the area last Tuesday in the most significant US challenge yet to territorial limits China claims around the Spratly archipelago.
The voyage triggered an angry rebuke from China and a warning that a minor incident in the area, one of the world's busiest sea lanes, could spark war if the United States did not stop what it called "provocative acts".
Abe told Park the situation in the South China Sea was "a common cause of concern for international society", Hagiuda told reporters.
In an apparent effort not to mar an incipient thaw in ties with China, the Japanese leader, speaking to reporters in Seoul, declined to specify whether he had raised the issue in bilateral talks with Chinese Premier Li Keqiang in Seoul on Sunday, following a meeting of the three North Asia leaders.