Doti Indrasanto, director of the Indonesian ministry's health affairs department, said that the recent deaths reported come as many previously reported as missing were considered dead.
"We have cross checked this information and it is correct," Indrasanto told the Reuters news agency.
The figures for those missing in Indonesia was reduced from 77,000 to 6,245.
In the Japanese city of Kobe Tuesday the U.N. head of emergency relief told a disaster prevention conference that many of the world's "megacities" are susceptible to devastating natural disasters.
"Perhaps the most frightening prospect would be to have a truly megadisaster in a megacity," U.N. director of disaster relief Jan Egeland told delegates from 150 countries Tuesday.
"Then we could have not only a tsunami-style casualty rate as we have seen late last year, but we could see 100 times that in a worst case," he added.
Megacities are considered those that have 10 million or more people in densely populated areas, usually including slums.
The five-day conference marked the 10th anniversary of an earthquake in Kobe where 6,500 people died.
Part of the meeting is geared toward developing a tsunami early warning system for the Indian Ocean similar to the one in the Pacific.
The U.N. Educational, Scientific and Cultural Organization proposed a system that would cost $30 million and could be operable by mid-2006.
While ideas for preventing future disasters continue, relief workers try to help victims from the tsunami in the midst of regional fighting.
A U.N. travel ban in the Indonesian province of Aceh has been lifted for aid workers. The 24-hour ban was issued after reports of fighting between government forces and rebels in Aceh, CNN reported.
Indonesia was hopeful to hold talks with rebels in Aceh where the Free Aceh Movement has been battling for three decades for a separate state.
"Behind the cloud there must be a silver lining. Behind the scenes, a process is happening toward reconciliation," Foreign Minister Hassan Wirajuda said, Reuters reported.
In Sri Lanka, regional strife has also played into relief efforts where the Tamil rebel-controlled northeast is waiting to learn if they will get some of the government's $3.5 billion relief money.
"The tsunami didn't wash away political divisions. In fact it may have made them worse," said Jehan Perera, director of the National Peace Council in Sri Lanka.
"What we have here is a moment that will define the peace process and politics for years," Perera said.