The two countries have a longstanding dispute over islands in the East China Sea controlled by Japan, which knows them as Senkaku, and claimed by China, which calls them Diaoyu.
Tokyo and Beijing agreed in June 2008 to cooperate over oil and gas resources in the area, but negotiations stopped two years later amid rising tensions and have not resumed.
"We confirmed that China is engaged in some kind of activity by stopping mobile drilling ships" near the median line separating the two countries' exclusive economic zones (EEZ) in the area, said Chief Cabinet Secretary Yoshihide Suga.
"It is extremely regrettable that China is unilaterally continuing its development activity," Suga, the government's top spokesman, told a press conference.
Foreign Minister Fumio Kishida made similar comments.
Suga added that Japan lodged the protest late last month after noticing the activity but did not specify what exactly the Chinese ships were doing.
Chinese drilling ships were last spotted near the median line in October 2016, Kyodo News and the Sankei Shimbun daily reported.
So far, China has built 16 drilling platforms on its side near the median line, the Asahi Shimbun reported.
Suga urged Beijing to resume stalled negotiations to jointly develop resources in the region, as discussed by Chinese President Xi Jinping and Japanese Prime Minister Shinzo Abe in September last year.
The gas field under the joint development agreement lies in an area where both countries' EEZs overlap.
Japan says the median line between the two nations should mark the limits of their respective EEZs.
But China insists the border should be drawn closer to Japan, taking into account the continental shelf and other features of the ocean.
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