Japan's Vice Foreign Minister Akitaka Saiki summoned the Chinese ambassador in Tokyo at around 2 a.m. (1700 GMT Wednesday) to "express a serious concern", the government said in a statement.
The Russian vessels were spotted around the same time a Chinese vessel entered the zone, the Kyodo news agency reported.
Japan administers the uninhabited isles under that name while China also claims them and calls them the Diaoyu islands.
Chief Cabinet Secretary Yoshihide Suga also criticized Beijing for escalating regional tensions. Meanwhile, the US said Chinese fighter planes unsafely intercepted a reconnaissance flight in worldwide airspace over the East China Sea, CNN reported. In the latest incident, however, maritime security operations were not ordered because the Chinese Navy vessel did not enter territorial waters.
The renewed tensions in the East China Sea, meanwhile, come after Japan used its role as host of the G7 meetings to criticize China and express opposition to any "intimidating, coercive or provocative" actions in both the East and South China seas, drawing an angry reaction from Beijing.
Gen Nakatani, Japan's defense minister, said Thursday he believes there "is a possibility that China aimed to show an uncompromising stance to its people and foreign countries based on its own assertion on territorial rights".
This was the first time a Chinese frigate entered the contiguous zone, he said.
The United States is strongly interested in China's intentions behind the entry of a Chinese Navy vessel into Japan's contiguous zone around the Senkaku Islands in Okinawa Prefecture. The US has sent warships past the reefs as a way to demonstrate that it does not recognize Chinese sovereignty.
Moreover, last week, Japanese Foreign Minister Fumio Kishida lodged protest with the Chinese embassy over China's continued construction of gas drilling rigs in the East China Sea despite the lack of finalization of 2008 bilateral agreement on the demarcation of a maritime boundary.