Mr Hishammuddin said in a statement: “Malaysia’s stand is clear – having friendly diplomatic relations with any countries does not mean that we will compromise on our national security.”
China’s embassy earlier said the planes conducted routine flight training and “strictly abided by” international law without violating airspace of other countries.
A spokesperson added: “China and Malaysia are friendly neighbours, and China is willing to continue bilateral friendly consultations with Malaysia to jointly maintain regional peace and stability.”
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 coastguard 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 exclusive economic zone (EEZ).
The Chinese embassy in Manila did not immediately respond to a request for comment outside business hours.
Tensions between Manila and Beijing have escalated over the months-long presence of hundreds of Chinese boats in the Philippines’ 200-mile exclusive economic zone. The Philippines says it believes the vessels were manned by militia, while Beijing has said they were fishing boats sheltering from bad weather.
“The Pag-asa Islands is an integral part of the Philippines over which it has sovereignty and jurisdiction,” the foreign ministry said in a statement.
Thitu, known as Pag-asa in the Philippines, is 451 km (280 miles) from the mainland and is the biggest of the eight reefs, shoals and islands it occupies in the Spratly archipelago.