Additionally, more ash-burned bodies have been discovered along the slopes of the mountain.
The volcano started erupting in late October after years of dormancy. The most significant blast was on November 5, when the majority of people died.
The agency says the volcanic activity has significantly declined and the current eruptions are not strong enough to endanger people.
On Saturday, half of nearly 400,000 evacuees have returned home. However, some 270,000 refugees remain in emergency camps because their homes were destroyed by the Mount Merapi explosion. Others, meanwhile, are without clean water and food.
With files from The Associated Press