Clouds of searing hot gases, debris and rock continued to avalanche down the mountain on Tuesday, but not as far or as often as they did on the previous day, when the most violent activity in several weeks was recorded.
The Indonesian president, Susilo Bambang Yudhoyono, on a visit to the threatened area, urged officials to be persistent in their efforts to move people away from the danger zone and warned residents not to assume their villages were safe.
"That is Merapi," said Ratdomopurbo, the region's chief vulcanologist. "She is always fluctuating."
Vulcanologists say as the clouds emerge from the crater their temperature can approach 1,000 degrees Celsius, although the heat drops rapidly once the gas shoots up into the air.
A large unstable lava dome perched on the crater formed by magma from within the volcano remained in place and could yet collapse, triggering a deadly surge in ash and gas, Ratdomopurbo said.
"Whatever happens, we are ready to face it. I have learned a lot from past disasters including the tsunami, and from that I can draw that if we conduct very good preparations ... there will be a lot that we can save"
Susilo Bambang Yudhoyono, Indonesia's president
Merapi, whose fertile slopes rise from the centre of Indonesia's densely populated Java Island, last erupted in 1994, sending a gas cloud 10 kilometres down its flank that incinerated 60 people.
At a search and rescue post near the mountain, the Indonesian president was briefed about evacuation efforts, disaster preparations, and the state of the volcano, which many hold sacred.
"Whatever happens, we are ready to face it. I have learned a lot from past disasters including the tsunami, and from that I can draw that if we conduct very good preparations ... there will be a lot that we can save," Yudhoyono said.
Indonesia was the nation hardest hit by the December 2004 tsunami. Around 170,000 Indonesians were killed or remain listed as missing.
Authorities raised the alert status of Merapi on Saturday to the highest level, known as code red or danger status, and Yudhoyono said 16,000 people have been evacuated.
"Let me say you are doing a good job," he told local emergency officials. "God willing, whatever happens, we can get over it."
Yudhoyono said while the government respected the beliefs of people in the area, it also had the responsibility of saving lives.
Many living on the slopes of Mount
Merapi believe it is sacred
He told refugees at one shelter that taking the mountain's course for granted could be risky.
"Better not return in a hurry ... the direction of the shaggy goat can't be ensured," he said, using the Javanese term for the deadly gas clouds. "Suddenly it might turn right or turn left."
But many villagers are reluctant to leave their homes and livelihoods and some who have left return during the day to tend livestock, collect grass, or otherwise carry on their daily routines.
And some people have dismissed the warning altogether.
Most Indonesians are Muslim, but many also follow animist beliefs and worship ancient spirits.
At full moon, they may trek to the crater's rim to throw in rice, jewellery and live animals to appease the volcano's spirits.
An 80-year-old man, appointed by the nearby royal court as Merapi's spiritual guardian, said he was not leaving even though his house is in the mandatory evacuation zone.
"There is no risk," Maridjan said outside his home, just six kilometres from the crater.
Authorities say Maridjan is setting a bad example.
Lynton Jaques, from Australia's geoscience agency, predicted "days or weeks" of activity at the peak and said that flows of ash, gas and debris - not a massive eruption - are the main threat to people.
The flows "are like a glowing avalanche that just incinerate everything in their path," he said.