'The relevant side should not make a fuss about nothing or over-interpret, it will be fine once they get used to it', ministry said.
Beijing: China told Japan on Friday to "get used to it" after it flew six warplanes over the Miyako Strait between two southern Japanese islands in a military exercise.
Japan's defence ministry issued a statement late on Thursday describing the flyover by the formation of Xian H-6 bombers earlier that day as "unusual", while noting that there had been no violation of Japanese airspace.
The Chinese navy and air force have in recent months carried out a series of exercises in the Western Pacific, as they hone their ability to operate far from their home shores.
The Chinese defence ministry said it was "legal and proper" for its military aircraft to operate in the airspace and that it would continue to organise regular training exercises according to "mission requirements".
"The relevant side should not make a fuss about nothing or over-interpret, it will be fine once they get used to it," the ministry said in a statement.
The Miyako Strait is between Japan's islands of Miyako and Okinawa, to the northeast of self-ruled Taiwan, which China claims as its own.
Taiwan's Ministry of National Defense said on Thursday the Chinese bombers flew just outside its air defence identification zone and that it had "closely followed" the movements.