China sent a special envoy, Song Tao, to the North last week but his four-day trip ended with no direct statement on the crisis, after Pyongyang's series of nuclear and missile tests triggered a global alarm.
China has denied any political motives behind its flag carrier's suspension of the route.
"The airliners just work out their own operation plans based on the state of operation and the market," foreign ministry spokesman Lu Kang said at a press briefing on Tuesday when asked about the apparent move.
Air Koryo also operates flights from the northeastern Chinese city of Shenyang to Pyongyang, though it halted flights from the Chinese border city of Dandong earlier this year.
Beijing is Pyongyang's only major ally and biggest trade partner, though in August China said it would abide by new UN sanctions which heavily curtail the North's exports of its most profitable goods.
The US on Tuesday unveiled new sanctions targeting North Korean shipping and Chinese traders doing business with Pyongyang, again raising the pressure on the pariah state to abandon its nuclear programme.