The first hot clouds were erupted at 8.11 a.m. on Friday to as high as 2,000 metres for 167 seconds and the next hot clouds were flowing at 8.18 a.m. to 1,500 metres high for 99 seconds, reports Xinhua news agency.
The third eruption of hot clouds were streaming down at 10.38 a.m. for 127 seconds.
Located between Yogyakarta and Central Java provinces, the status of the 2,968-metre high volcano is currently at its third level of danger.
The centre has urged people not to move to the dangerous zone within a radius of 3 km from the volcano's peak and to stay away of rivers that flow from Merapi, such as Kuning, Boyong, Bedog, Krasak, Bebeng and Putih rivers.
The volcano's 2010 eruption killed more than 200 people and forced hundreds of thousands to flee their homes.
Indonesia has 127 active volcanoes and about 5 million people within the danger zones.