Indonesia's earthquake survivors will need a six-month relief operation costing more than $100m, UN officials have said.
The UN says more than half the aid should be spent on housing
Georg Peterson, from the WHO, said the challenge in the short term was to get people out of crowded hospitals to prevent the spread of infection.
Friday prayers were held in the area for the first time since the quake hit, killing at least 6,200 people.
Many Javanese believe last Saturday's disaster was a warning from God.
"The height of the emergency phase will continue, I would expect, for another week to two weeks, and at the most be completed in a month," Charlie Higgins, UN aid co-ordinator in the area, told a news conference.
"The area, although not large, is constricted and there are many difficulties in moving relief to difficult areas," he said.
But an estimated $100m ($78m) will be needed over the next six months, and nearly half of that money should go toward housing, according to the UN Office for the Co-ordination of Humanitarian Affairs.
Religion plays an important role in many locals' lives
Thousands of local Muslims attended prayers on Friday.
In the village of Giwangan, on the southern outskirts of Yogyakarta, a special prayer leaflet was distributed entitled "Disaster and How to Face It", quoting a passage from the Koran saying natural disasters were God's will.
"We want to make peace inside by praying and being closer to God," local merchant Iskak, 40, told the French news agency AFP.
"The earthquake is because God would like to give a warning to people, that it is the fault of humankind."
Sukasdi, a 51-year-old police officer, said his survival had strengthened his faith.
"I feel that my life is more valuable because my life has been given to me by God. I feel much closer to God and I can face the situation in a more peaceful way," he said.
At least 30,000 people were injured and more than 105,000 homes destroyed or damaged by the quake, leaving hundreds of thousands of people displaced.
Mr Peterson, from the World Health Organization, said that many of those who had died in recent days were elderly people who had suffered complications from their injuries or infections of their wounds.
The 6.3 magnitude quake hit the ancient city of Yogyakarta early on Saturday.
The region is close to the volcano Mount Merapi which has been spewing lava and ash for some weeks.