According to state news agency Bernama, Shahidan said assets from the Malaysian Maritime Enforcement Agency and the navy have been deployed to the area to monitor the situation.
China claims most of the South China Sea through which about $5 trillion in ship-borne trade passes every year. Neighbours Brunei, Malaysia, the Philippines, Taiwan and Vietnam have rival claims.
Malaysia would take legal action if the ships were found to have trespassed into the country's exclusive economic zone, Shahidan was quoted as saying.