A defence ministry spokesman said a Chinese Su-27 jet yesterday flew close to a Japanese OP-3C surveillance plane above the waters where the countries' air defence identification zones overlap.
Another Chinese SU-27 fighter also flew close to a Japanese YS-11EB plane in the same airspace, the ministry said.
One fighter jet approached to within about 50 metres and the other was as close as 30 metres to the Japanese planes, according to the spokesman.
Beijing raised regional tensions in November by declaring an air defence identification zone covering the area, which overlaps a similar Japanese zone.
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"They were dangerous acts that could lead to an accident," Japanese Defence Minister Itsunori Onodera told reporters today.
"The Japanese crew reported that the fighters were flying with missiles, which raised the tension as they handled the situation."
Tokyo protested to Beijing over the incident through diplomatic channels, he said.
The Chinese fighters did not enter the Japanese zone, according to the Asahi Shimbun daily.
Chinese state-owned ships and aircraft have periodically approached the Senkaku islands, which China also claims and calls the Diaoyus, to assert Beijing's claim to them.
China's defence ministry said two Japanese planes entered China's air defence identification zone yesterday, "interfering with joint naval exercises between China and Russia" for which a "no fly" notice had been issued.
Chinese aircraft were scrambled to "identify and take protective measures" against the Japanese planes, the ministry said in a statement on its website.