Flight tracking website FlightRadar24 showed few commercial flights over Afghanistan at 3 am GMT on Monday but many planes overflying neighboring Pakistan and Iran.
The website, which tracks flights in real-time, also showed Singapore Airlines (SIA) flight SQ 319 from London to Singapore avoiding Afghan airspace.
United Airlines, British Airways, and Virgin Atlantic said they were not using the country's airspace.
A United spokeswoman said the change affects several of the airline's US to India flights.