Massive plumes of dark ash are still billowing two miles above the summit of the rumbling volcano, which has been erupting for days.
And with Agung continuing to spew columns of ash and toxic gas into the skies it could be weeks before flights return to normal.
Some Qantas passengers have reportedly been told their flight have already been rescheduled to take off until after Christmas.
Agung last erupted in 1963 when it killed 1,100 people. However, after the initial blast it remained "active" for the next 11 months.
Besides the ash, and gas local are now tackling a new hazard – toxic rivers of lahar – deadly mudflows made up of volcanic debris.
Lahars flow like liquids, but because they contain rubbish and debris, they usually have a consistency similar to wet concrete.
They can travel at speeds of over 50 mph and reach distances dozens of miles from their source.
Some 40,000 people have abandoned their homes in the danger zone but as many as 100,000 will likely be forced to leave, disaster agency officials have said.
"Volcanic ash is still spewing. It's thick and rising very high – up to three or four kilometres from the crater," said Gede Suantika, an official at Indonesia's volcanology agency.
The exclusion zone around Agung, which is 50 miles from the beachside tourist hub of Kuta, has also been widened to six miles.
As of Tuesday, some 443 flights had been cancelled, affecting more than 120,000 passengers.
Inn operator Wayan Yastina Joni was among the few hoteliers willing to take up an appeal by Bali's governor and tourism agency to supply free rooms to the thousands.
"I don't mind giving free accommodation for tourists I already know," said the owner of the Pondok Denayu Homestay.
"This is nobody's fault. It's a natural disaster that no one expected," he added.
Hundreds of tourists are now being shuttled to Indonesia's second city Surabaya, about 13 hours' drive away, so they can fly out of the country.
"We are preparing 10 busses and more can likely be provided later today," said Bali Transportation Agency Head Agung Sudarsana.
Mount Agung's last eruption in the early sixties was one of the deadliest ever seen in a country with nearly 130 active volcanoes.
"I am very worried because I have experienced this before," 67-year-old evacuee Dewa Gede Subagia, who was a teenager when Agung last roared, told AFP.
"I hope this time I won't have to evacuate for too long. In 1963, I left for four months."
Indonesia is the world's most active volcanic region. The archipelago nation with over 17,000 islands lies on the Pacific "Ring of Fire" where tectonic plates collide, causing frequent volcanic and seismic activities.
Last year, seven people were killed after Mt. Sinabung on the western island of Sumatra erupted. A 2014 eruption at Sinabung killed 16.
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