The agency also said it had raised the warning level on the peak to an unprecedented 4 (prepare to evacuate), from 3.
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The Sakurajima volcano is located about 50 kilometres (31 miles) from the Sendai nuclear power plant, which was the first nuclear facility to restart one of its reactors earlier this month, after new safety rules were introduced in Japan following the 2011 Fukushima nuclear disaster. It detected multiple earthquakes in the area on Saturday morning, the agency said on its website.
Critics have said the restarted reactor at Sendai was still at risk from natural disasters.
Officials in Japan are preparing for what could be a large explosive eruption from Sakurajima.
The warning applies to a part of the island, which is home to more than 4,000 people.
The last eruption of the popular tourist site came in 2013, when it spewed ash around 5,000 meters (16,400 feet) into the air, causing damage but no major injuries.
Japan lies on the so-called “Ring of Fire”, an arc of volcanoes and fault lines surrounding the Pacific Basin, and it sits at the three-way meeting point of the North American, Eurasian and Philippine Sea tectonic plates.
Last September, almost 60 people died when Mount Ontake, located on the Honshu island, erupted.
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The shock eruption was Japan’s deadliest for nearly 90 years, leaving an estimated 63 people dead, many of their bodies at least partially entombed in volcanic sludge.
