The volcanic island of Anak Krakatau, in Indonesia's Sunda Strait between the main Java and Sumatra islands, had showed signs of activity since Friday before erupting for 30 seconds early on Sunday and for 16 seconds about three hours later, Indonesia's Geological Agency said.
Closed-circuit camera footage showed lava flares from the volcano.
No casualties were reported and no evacuation order was issued.
The nearest settlement is more than 16km away, but authorities warned residents and visitors to stay at least three kilometres from the active crater.
Volcanic ash spread across parts of Jakarta and Lampung province on Sumatra's southern tip, Indonesia's Center for Volcanology and Geological Hazard Mitigation said.
AirNav Indonesia closed airspace around Soekarno-Hatta and Halim Perdanakusuma airports in Jakarta, as well as six other airports, including Radin Inten II Airport in Lampung, because of volcanic ash.
By Sunday evening, the closure of eight airports had affected 170,000 passengers from 1558 cancelled flights, including 963 flights in Jakarta's Soekarno-Hatta airport alone.
Indonesia's Directorate General of Civil Aviation said it was closely monitoring the eruption's impact on air travel and co-ordinating with airlines, airport operators, air navigation services and the meteorology agency.
"Safety remains our top priority in every operational decision," Lukman F Laisa, Ministry of Transportation director general of civil aviation, said in a statement.
He warned flight schedules could face cascading disruptions affecting aircraft rotations, fleet availability and terminal capacity as airlines work to restore operations.
The eruption also disrupted services at Bali's Gusti Ngurah Rai International Airport and at Medan.
Indonesia's volcanology agency and the Darwin Volcanic Ash Advisory Centre identified two ash clouds using satellite imagery.
One plume rose to 6100 metres and drifted northeast over Jakarta, Banten, West Java and nearby waters.
A second cloud reached 15,200 metres and spread over parts of Banten, Lampung and Bengkulu provinces, the southern Sunda Strait and sections of the Indian Ocean west of Sumatra.
Lana Saria, head of Indonesia's Geological Agency, said activity at Anak Krakatau has intensified since July, with Sunday's eruption the strongest during that period.
The repeated eruptions indicate a continued supply of magma and volcanic gases beneath the volcano, she said, though officials can't predict whether a larger eruption will occur.
"We continue to evaluate the volcano's development based on all monitoring data, not solely on the number of eruptions or the height of the ash column," Saria said in a video briefing.
The main hazards include volcanic ash, high concentrations of gas and the ejection of hot rocks and other material around the crater area.
