Flights have resumed over northern Australia as major ash plumes cleared from an Indonesian volcanic eruption that stranded thousands of passengers.

The city of Darwin was completely cut off from air traffic yesterday by ash clouds drifting from the Sangeang Api volcano, forcing the cancellation of dozens of flights.

Passengers hoping to travel to Bali from Australia's west coast were also impacted by the plume.

Darwin airport said flights had resumed this afternoon, with national carrier Qantas Airways confirming it had restarted operations and budget airlines Jetstar and Virgin also set to return to the skies.

"Flights are coming back online but there are some scheduled changes so people still need to check with the airline with regards to what's happening with their particular flight," a Darwin airport spokeswoman said.

Air services Australia, the government's airspace agency, said the plume had continued to dissipate overnight and throughout the day and skies were clearing.

"The ash plumes that may have affected flights into and out of Cairns and Townsville today have dispersed and will not affect flights. Brisbane flights will also be unaffected," the agency said.

"Decisions on whether or not flights will operate will be made by individual airlines and operators based on a careful assessment of all available information," it said.