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Malaysia's air force said it scrambled jets on Monday to conduct visual confirmation after the planes flew within 60 nautical miles off Sarawak state of Malaysian Borneo.
It described the incident as a "serious threat to national sovereignty and flight safety."
The Chinese planes did not contact regional air traffic control despite being instructed several times, the air force said.
Foreign Minister Hishammuddin Hussein said Malaysia will issue a note of diplomatic protest and ask China's ambassador to Malaysia to explain the "breach of the Malaysian airspace and sovereignty."
"Malaysia's stand is clear -- having friendly diplomatic relations with any countries does not mean that we will compromise on our national security," Hishammuddin said in a statement.
China's embassy earlier said the planes conducted routine flight training and "strictly abided by" international law without violating airspace of other countries.
"China and Malaysia are friendly neighbors, and China is willing to continue bilateral friendly consultations with Malaysia to jointly maintain regional peace and stability," a spokesperson said.
China has been pushing an expansive claim over the South China Sea, through which about $3 trillion worth of ship-borne trade passes annually. It has also built military facilities on manmade islands.
Brunei, Malaysia, the Philippines, Taiwan and Vietnam also have claims to various islands and features in the area and China's coast guard routinely warns foreign boats and aircraft to leave what it calls its territory.
Malaysia's air force said the planes, comprising Ilyushin il-76 and Xian Y-20 strategic transporters, had traveled in an "in-trail" tactical formation at between 23,000 and 27,000 feet.
Last year, a Chinese survey ship held a month-long standoff with a Malaysian oil exploration vessel within Malaysia's EEZ.