Pyongyang has drawn criticism from Seoul and Washington for firing half a dozen short-range missiles off its east coast in recent days, followed by a volley of rockets from multiple launchers.
South Korea said a Chinese airliner with more than 200 passengers on board crossed the trajectory of one of the rockets seven minutes after it passed by.
China is North Korea's key diplomatic protector and the source of much of its trade and aid.
"I want to stress we attach high importance to the security of national civil airlines," Beijing's foreign ministry spokesman Qin Gang said.
Countries should take "necessary measures" when carrying out military drills "to ensure the security and safety of civil ships and aircraft", he said.
"Without any doubt, China will verify the relevant situation with the relevant party and express necessary concerns over that," Mr Qin.
Seoul's defence ministry said China Southern Airlines flight CZ 628 from Tokyo to Shenyang in northeast China crossed the flight path of the rocket, describing it at a "provocative act" by the North and a "grave" threat to civilian security.
The missile and rocket tests were largely seen as a calculated display of military muscle-flexing to reflect the North's anger over ongoing South Korea-US military exercises.
The North's military defended the tests on Wednesday, calling them "ordinary military practice".