The Chinese vessels entered the area yesterday and were still there this morning, the foreign ministry said, marking the longest incursion since the long-simmering dispute erupted again last year.
Tokyo issued a protest to acting ambassador Han Zhiqiang over the latest incident, a Japanese foreign ministry spokesman told AFP.
"The Chinese side argued its... Position and said it could not accept Japan's protest," he said after the Chinese diplomat met Japanese officials.
The incursion was the latest in a series by Chinese government ships in recent months around the Senkaku islands.
China issued strong criticism after Japan on Tuesday unveiled its biggest warship since World War II, a $1.2 billion helicopter carrier aimed at playing a major role in disaster and rescue missions, as well as defending sea lanes and Japanese territory.