VP Corporate of PT Garuda Indonesia Hengki Heriandono said Garuda Indonesia will continue to monitor the situation and developments related to the activities of Mount Agung, especially the activity of the spread of volcanic ash that can disrupt flight safety.
The alert status was not changed from a level 3 alert, its second-highest level, despite the latest eruption, Spokesman Sutopo Purwo Nugroho said.
"Once the airports find volcanic ash trace, we'll close down the airport for flights", said Herson, chief of Bali's Ngurah Rai airport. Virgin Airlines cancelled several flights between the island and Australia.
The island's main airport is for now operating normally, but some airlines have cancelled flights.
The flights of about 5,000 passengers were cancelled on Sunday and another 2,500 holidaymakers could not get in because their planes were rerouted or never took off.
Staff at Indonesia's volcano monitoring centre said it was not just pulverised rock being blown out of Mt Agung, but magma has now reached the volcano's surface.
"All flights are back to normal", said Herson, head of the local airport authority, who uses one name.
Mount Agung erupts for the second time
It told people within a 7.5km exclusion zone to "immediately evacuate" in an "orderly and calm manner".
While many have since returned, more than 25,000 people remain evacuated in over 200 temporary shelters.
During its last eruption in 1963 it left more than 1,000 people dead and destroyed several villages.
It is home to more than 130 active volcanoes.
Mount Agung's alert status was raised to the highest in September following a dramatic increase in tremors from the volcano, which doubled the exclusion zone around the crater and prompted more than 140,000 people to leave the area.
Indonesia sits on the Pacific "Ring of Fire" where tectonic plates collide, causing frequent seismic and volcanic activity.