Singapore Airlines said it had cancelled a flight on Wednesday from Bali to Singapore due to the eruption.
Bali is Indonesia's top tourist hotspot and is a popular destination for Australian visitors.
All flights to and from the island of Lombok in the West Nusa Tenggara province, another popular destination for tourists, were also cancelled, a local airport spokesperson was quoted as saying by Indonesia's state news agency Antara.
Indonesia has close to 130 active volcanoes and sits on the Pacific "Ring of Fire", an area of high seismic activity atop various tectonic plates.
The ash column from Mount Lewotobi has reached as high as 10 km and authorities have said sand fall has covered surrounding areas.
MA/PR