The two eruptions lasted around seven minutes, according to the agency, and prompted local authorities to order residents to stay outside a three-kilometre no-go zone around the rumbling crater near Indonesia's cultural capital Yogyakarta.
The agency did not raise the volcano's alert status after the eruptions, but it advised commercial planes to be cautious in the area.
Local media reported that people in neighbouring areas including Sleman and Klaten heard strong rumbling sounds this morning.
Villagers living on Merapi’s fertile slopes are advised to stay 3km (1.8 miles) from the crater’s mouth and should be aware of the peril of lava, the agency said.
Mount Merapi's last major eruption in 2010 killed more than 300 people and forced the evacuation of some 280,000 residents from surrounding areas.
That was its most powerful eruption since 1930, which killed around 1,300 people, while another explosion in 1994 took about 60 lives.
Indonesia has more than 17,000 islands and islets -- and nearly 130 active volcanoes.
The South-East Asian archipelago nation sits on the Pacific "Ring of Fire", a vast zone of geological instability where the collision of tectonic plates causes frequent quakes and major volcanic activity. - AFP
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