The volcano's lava dome has swelled in recent weeks, raising concerns that it could suddenly collapse and send scalding clouds of fast-moving gas, lava and rocks into populated areas.
Some scientists say a powerful May 27 earthquake that killed more than 5,700 people in area just 40 kilometers (25 miles) south of Merapi may have contributed to the increased activity at the volcano, the AP reports.
Subandriyo said the mountain appeared a little calmer than on Monday and Tuesday, but that it was in a state of flux.
Indonesia's disaster management office said 3,000 people were evacuated from the mountain Wednesday, bringing the number who left since the alert level was raised to its highest level three weeks ago to nearly 23,000.
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