Tokyo summoned China's envoy on Tuesday in protest after what it says was another incursion into its territorial waters around islands at the centre of a bitter dispute with Beijing.
"The foreign ministry summoned the Chinese ambassador over ships entering the waters near Senkaku islands," said a foreign ministry official, referring to a chain claimed as the Diaoyus by Beijing.
The move comes after Chinese state vessels spent much of Monday in waters around the islands and as the two sides show no sign of backing down in a dispute that has badly affected trade between Asia's two largest economies.
Two maritime surveillance boats arrived in the area shortly before 9:30 am (0130 GMT), the Japanese coastguard said, with Kyodo News reporting they had remained there for around 14 hours.
Chinese ships have repeatedly ventured into the waters, in what observers say is Beijing's bid to create a "new normal" in which Tokyo does not have effective control over the archipelago.
A Chinese government plane entered the chain's airspace in December, setting off sorties by Japanese fighter jets.
In recent weeks both countries have dispatched military planes to the region, although there have been no clashes.
But analysts say the ramping up of rhetoric and the more frequent confrontations raise the risk of an accidental armed conflict.