State broadcaster CCTV reported last Friday that Air China had suspended its Beijing-Pyongyang route, leading to speculation the move was intended to pressure the North.
But foreign ministry spokesman Lu Kang distanced his government from the decision and said it was purely 'market-based'.
"It's natural for Air China or other airlines to make such decisions," Mr Lu told a regular press briefing. "There shouldn't be overinterpretation of this issue".
Beijing is Pyongyang's only major ally and biggest trade partner. It is being urged by the Trump administration to do more to rein in the North's missile and nuclear weapons programmes.
In February China announced it was halting all imports of coal from North Korea - a crucial earner for Pyongyang - for the rest of the year.
A customer service representative for Air China, the only foreign carrier operating a regular commercial flight to North Korea, said Monday it had cancelled the flights due to low demand.
"Air China has not suspended operations for the Beijing-Pyongyang route," the employee told news agency AFP, adding "these flights were cancelled based on ticket sales."
An operator reached through the airline's customer service hotline said the booking system indicated that the earliest available Beijing-Pyongyang flight was for March next year.
Travel disruption also hit North Korea's flag carrier Air Koryo, which saw its Beijing-bound service delayed more than ten hours on Monday.
Workers at Pyongyang airport told passengers the delay was weather-related, although conditions in the area and in Beijing appeared clear.
"We didn't receive any request to take the trips off the shelf - the reason was poor sales," Wang Mi, a spokeswoman for the online travel company Tuniu.com, told news agency AFP.
Gan Tingting, a spokeswoman for tourism booking site Lvmama.com, said trips to North Korea had long been discontinued because the country was "not a hot destination".
Foreign companies bringing tour groups to North Korea, however, have seen no dip in demand.
"We're business as usual," said Matt Kulesza, media officer for Young Pioneer Tours.
Beijing-based Koryo Tours likewise said in a statement that none of their tours have been cancelled or cut short.
"There have been no issues with our scheduled Air Koryo flights or the train back into China," it said.
President Donald Trump has personally underscored the importance of China's cooperation in tackling North Korea.
Having blasted Beijing throughout his presidential campaign for alleged currency manipulation, he tweeted Sunday, "Why would I call China a currency manipulator when they are working with us on the North Korean problem? We will see what happens!"