Itsunori Onodera's comments are likely to further heighten fears that the two countries could be sliding towards conflict over the outcrops in the East China Sea.
"I believe the intrusions by China in the territorial waters around the Senkaku islands fall in the 'grey zone' (between) peacetime and an emergency situation," Onodera told reporters in Tokyo.
The two sides have been at loggerheads over the island chain, claimed by China as the Diaoyus, since Tokyo bought three of them from their private Japanese owner in September 2012.
But the comments from Onodera following those from China's defence ministry at the weekend, appear to have taken the verbal fisticuffs to a new level.
On Monday, China's coastguard sent four vessels into the waters around the islands, where they stayed for two hours, shadowed by their Japanese counterparts.
That came after three consecutive days in which Tokyo scrambled its jets to meet Chinese aircraft flying near to Japanese airspace as they traversed a strait that leads into the Pacific.
"They were two early-warning aircraft and two bombers," Onodera told reporters on Tuesday.
"It was unusual that so many aircraft flew between the Okinawan main island and Miyako island. We consider that it is also very unusual that it occurred for three days in a row.
"We understand that it is one of the trends showing that China is now vigorously expanding its areas of activities, including into the open ocean."
Last week it was reported that popular Prime Minister Shinzo Abe had given the green light to plans to fire on any unmanned aircraft that did not heed warnings to leave Japanese airspace.
That came after officials said an unidentified drone was logged on a trajectory towards southern Japan. Tracking stations noted that the craft appeared to have come from, and returned to, Chinese airspace.
Privately, policy-makers said there was no doubt about its origins and pointed out that China is known to be developing its drone fleet.
China's defence ministry said on Saturday that Japan's firing on its aircraft "would constitute a serious provocation, an act of war of sorts".
"We would have to take firm countermeasures, and all consequences would be the responsibility of the side that caused the provocation," it said.
Observers warn that the frequent presence of armed vessels and aircraft in the area raises the risk of a confrontation, and point out that a minor slip by a crew member on either side could quickly escalate.
Tokyo announced last week that it was planning a huge drill on an island hundreds of kilometres (miles) away, starting Friday, intended to sharpen the skills of 34,000 troops in defending -- and retaking -- distant territory.
It has also upped its global PR campaign with the posting on YouTube of videos putting its case for sovereignty of the Senkakus and a separate pair of islands at the centre of a dispute with South Korea.
The recent manoeuvres were the latest in a long line of actions and reactions in the bitter scrap with China, which is putatively about the uninhabited islands but is fuelled by historical animosities and nationalism.
Japan says it annexed unclaimed islands in 1895 and maintains China's claims of ownership date only from the discovery of fossil fuel reserves in the nearby seabed at the end of the 1960s.
China says the islands have been a part of its "inherent" territory for hundreds of years and maintains Tokyo's annexation was an early move in its imperial expansionism in Asia, culminating in World War II.