The two countries both claim islands in the East China Sea controlled by Japan, which knows them as Senkaku, and regularly send ships to nearby waters to assert their claims amid repeated diplomatic clashes.
Talks between Tokyo and Beijing begun in June 2008 to cooperate over oil and gas resources in the area broke down two years later amid rising tensions, and have not resumed.
On Tuesday, Japan's top government spokesperson Yoshihide Suga told reporters it was "extremely regrettable that China is unilaterally continuing its development activity" by stopping mobile drilling ships near the median line separating the two countries' exclusive economic zones (EEZ).
He added that Japan lodged a protest late last month after noticing the activity but did not specify what exactly the Chinese ships were doing.
"China's oil and gas activities in the East China Sea are all located in maritime areas indisputably under Chinese jurisdiction," China's foreign ministry told AFP in a statement, adding: "The so-called issue of 'unilateral exploitation' does not exist."
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.
China's foreign ministry said it rejected the idea of a median line between Japan and China, calling it "Japan's unilateral proposition."
Chinese drilling ships were last spotted near that 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.
Earlier this year, US President Donald Trump offered reassurances the US would come to Japan's defence if China were to seize the uninhabited Senkaku islets, which it calls Diaoyu.
In a joint statement with Japan's Prime Minister Shinzo Abe in February, the pair said they "oppose any unilateral action that seeks to undermine Japan's administration of these islands".
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)