Ash from Anak Krakatau, which sits halfway between Java and Sumatra islands, has blanketed Jakarta and several surrounding areas since it erupted late on Friday, leading to the closure of the airports for safety reasons.
The transport ministry said the closure of eight airports had affected 170,000 passengers from 1,558 cancelled flights, including 963 flights in Jakarta's Soekarno-Hatta airport alone.
Jakarta's main airport will remain closed until 6pm on Monday (9pm AEST), its operators said on Instagram.
"We cannot ascertain when this will end due to the dynamic weather," Transport Minister Dudy Purwagandhi said in a statement, adding the seven other airports, which included the ones serving Jakarta's nearby provinces of Lampung and West Java, would also remain closed.
The volcano monitoring agency's website showed the most recent Anak Krakatau eruption occurred on Sunday evening.
The agency warned on Monday that "the probability of further eruptions in the coming periods remains high".
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.
The eruptions have seen ash reach as high as 6000 metres on the Java side of the volcano and 15,000 metres on the Sumatra side and some parts of Banten province in Java, meteorological agency BMKG posted on its website.
Indonesia's Directorate General of Civil Aviation said that 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 disaster agency called for people to wear masks while travelling outdoors to avoid breathing in the ash.
In Jakarta and Lampung, schools will use remote learning to counter health risks for students, state news agency Antara reported.
Indonesia sits on the Pacific "Ring of Fire", where earthquakes and volcanic eruptions are frequent.
Anak Krakatau, which means child of Krakatau, began emerging a century ago from the area previously occupied by Krakatau, then known as Krakatoa.
The older volcano destroyed itself in mass eruptions in 1883, which killed more than 36,000 people in a series of tsunamis.
with AP
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