The company confirmed to the BBC that crew witnessed "what is suspected to be the re-entry" of the missile into the earth's atmosphere.
It added that as things stand no flight routes were being modified.
On 29 November North Korea tested a new intercontinental ballistic missile it said could reach anywhere in the US.
The test-launch raised tension further with South Korea and the US, who on Monday began their largest ever joint air exercise, which the North has branded an "all-out provocation".
'Blew up and fell apart'
Described by Pyongyang as its "most powerful" missile, the 29 November launch ended up in Japanese waters but flew higher than any other the North had previously tested.
According to the South China Morning Post, Cathay's general manager of operations Mark Hoey told staff in a message that "today the crew of CX893 reported, 'Be advised, we witnessed the DPRK missile blow up and fall apart near our current location'".
The launch was reportedly also witnessed by two South Korean aircraft en route to Seoul from the US.