The volcanic island emerged from the sea at the beginning of the last century from the crater formed after the 1883 eruption of Mount Krakatoa -- one of the deadliest and most destructive in history.
Anak Krakatoa, which means "Child of Krakatoa", spewed thick ash over the strait that separates the islands of Java and Sumatra.
There were no immediate reports of damage or casualties after the eruption at 08:46 am (0146 GMT).
"The height of the eruption column was observed to be 3,000 metres (nearly 10,000 feet) above the summit," Deny Mardiono, an official from the Krakatoa monitoring station, said in a press release.
"The ash column was observed to be grey to black with thick intensity to the southwest."
He warned the public not to carry out activities within a five-kilometre (three-mile) radius of the volcano's crater.
Anak Krakatoa's status was at the second-highest warning level after authorities raised it in 2022 following a sharp rise in volcanic activity.
Its crater partly collapsed in 2018 when a major eruption sent huge chunks sliding into the ocean, triggering a tsunami that killed more than 400 people and injured thousands.
Indonesia, a Southeast Asian archipelago nation, sits on the Pacific Ring of Fire, where the meeting of continental plates causes high volcanic and seismic activity.
The country has nearly 130 active volcanoes.
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