Siti Fadillah Supari, Indonesia's health minister, said on Wednesday the government was also moving patients from hospitals in the immediate area to more distant cities to relieve overcrowding.
"For now [the hospitals] are starting to get tidy and we have penetrated isolated areas using mobile clinics ... helicopters dispatch food while airlifting the patients. The supply of medicine is also flowing," she said.
"Today we are continuing to comb [the region] to make sure there are no untouched areas."
The toll from Saturday's quake rose to 6,234 after officials found 388 more bodies, social affairs ministry spokesman Juswadi said on Wednesday. At least 30,000 were injured and 647,000 people have been displaced.
So far there are no signs of any outbreaks of disease, but medicines were being sent to affected areas to prevent diseases such as malaria.
The 6.3 magnitude quake, which was centred just off the Indian Ocean coast near Yogyakarta, wrecked some infrastructure such as water pipes and pumps. Damage to roads is hindering efforts to distribute aid.
Around the Bantul area, which was hardest hit, entire villages were destroyed, homes reduced to piles of wood, tiles and tin, and survivors used whatever they could find to construct shelters.
Haruhiko Kuroda, the Asian Development Bank president, said late on Tuesday that Susilo Bambang Yudhoyono's government had learnt from the Indian Ocean quake and tsunami in December 2004 that left 170,000 Indonesians killed or missing.
"This time the government was very quick in responding to the need," Kuroda said.
Dozens of countries have pledged cash, emergency supplies and personnel, and UN agencies and private international organisations such as the Red Cross began moving aid in shortly after Saturday morning's quake.
Dozens of countries have vowed
to send cash and relief supplies
Much of the aid is being airlifted to the airport of the ancient royal capital of Yogyakarta, the main city in the afflicted area.
But on Wednesday morning in the Bantul area, residents of Sampangan Kidul village said proper shelter and goods were still slow in coming.
Edward Beigbeder, head of the UN children's fund operation in Yogyakarta, said that incoming aid was insufficient to meet demand. "We're doing a race against the clock," he said.
The government has set aside relief funds of 100 billion rupiah ($10.86 million) for the next three months. This will be followed by a year of reconstruction and rehabilitation.