The volcano, situated in the main Java Island, started erupting at 10:56 am (Jakarta time), the Center for Research and Development of Geological Disaster Technology of the Volcanology Agency in Yogyakarta province said in a statement.
The wind blows to the southwest of the crater, it said.
The agency heightened the volcano observatory notice for aviation (VONA) to the highest level with a red code from the green-code normal level.
The red code means that planes are banned from flying through the air space above the area around the volcano.
Residents are prohibited from having activities in a radius of 3 km from the crater.
The volcano last erupted on March 3, spewing a column of ash of up to 6km to the sky.
The 2,930 meter-high Mount Merapi, one of Indonesia's 129 active volcanoes, has regularly erupted since 1548.
During its eruption from October to November 2010, a total of 353 people were killed and about 350,000 others were forced to evacuate.
Indonesia, a vast archipelagic nation, is prone to volcanic activities and earthquakes as it lies along the so-called "Pacific Ring of Fire".
