Its public relations department said 26 worldwide inbound and outbound flights had been cancelled, affecting almost 5,000 travellers.
The early morning closure of Ngurah Rai airport sparked the cancellation of almost 280 flights to and from the tropical paradise with some 15,700 passengers affected, according to revised figures from an airport spokesman.
Operations at Bali's airport were disrupted for more than a week in early December, stranding thousands of visitors before winds changed to blow the smoke away and the volcano calmed down.
Two other airports in East Java were also ordered closed on Friday, according to DPA news agency.
"Safety remains the main reason for the decision to close the airport", disaster management spokesman Sutopo Purwo Nugroho said in a statement.
The airport had been closed since 3 a.m. local time on Friday.
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Activity at the volcano was high last year and forced the evacuation of tens of thousands of people, but it had been quieter this year. "We just miss the kids", he added. Authorities are still scrutinising the situation and have not raised the alert level yet.
There is a 4km no-go zone around Agung's peak.
Bali's governor said officials were working on getting visitors on their way.
The volcano, about 70km northeast of Bali's tourist hotspot of Kuta, last had a major eruption in 1963, killing about 1100 people.
"There have been a number of events world-wide recently, such as earthquakes, tsunamis and volcanoes, which highlights the importance of travel insurance and so we recommend anyone soon to travel overseas to make sure they have sufficient cover for their trip, " she said.
The crater has been erupting periodically since it rumbled back to life past year.