The ministry raised the country's toll to 166,320 on Wednesday. It had previously given a figure of 95,450 while Indonesia's Ministry of Social Affairs had put the toll at about 115,000 before it stopped counting.
Dodi Indrasanto, a director at the Health Ministry's department of health affairs, said the new total reflected the latest reports from the provinces of Aceh and north Sumatra, which were directly in the path of the killer tsunami spawned by a huge earthquake the day after Christmas.
The new figure lifted the total global toll from the disaster to 226,566, although the number continues to rise as more deaths are reported around the region.
Indonesian President Susilo Bambang Yudhoyono, speaking before the Health Ministry released its latest figures, told a donors conference in Jakarta that the true extent of the catastrophe defied description.
"Perhaps we will never know the exact scale of the human casualties," he said.
Indrasanto said the health ministry report, which had 6245 people still listed as missing, had been sent to Susilo late on Wednesday.
The disaster in Aceh has affected
negotiations with rebels
The ministry's figures said 617,159 people were still homeless in northern Sumatra more than three weeks after the killer wave struck.
The staggering death count came as Indonesia said it was hopeful of holding talks with rebels in Aceh, where the Free Aceh Movement (GAM) has waged a decades-long battle for independence from Jakarta's rule.
"Behind the cloud there must be a silver lining. Behind the scenes, a process is happening towards reconciliation," Foreign Minister Hasan Wirajuda said.
He said he hoped the talks would take place by the end of the month, but could give neither a date nor a place. A spokesman for GAM's exiled leadership in Sweden said there had been no progress on talks.
"We haven't had any concrete response from the Indonesian side," said Bakhtiar Abd Allah.
"Behind the cloud there must be a silver lining. Behind the scenes, a process is happening towards reconciliation"
Foreign Minister Hasan Wirajuda
A UN official in Meulaboh, the province's second city, said emergency aid drops would have to be sharply increased to avoid hunger in outlying areas.
Security fears prompted by the GAM conflict have been a worrying backdrop to the massive international relief effort in Aceh, with Jakarta insisting all aid groups must have Indonesian army escorts.
But GAM's leaders have repeatedly welcomed relief efforts spearheaded by the United Nations, and the rebels have said they would not attack aid workers or convoys.
Speaking from the Sri Lankan coastal city of Galle on Thursday, Ahmed al-Shaikh, Aljazeera's representative in Sri Lanka, said: "The scenes we have seen in Galle are really painful.
"We set off early in morning from Colombo to Galle in the south, which is the nearest point we could reach, before planning to return to Colombo to follow up on our trip to Aceh.
A South Korean aid worker uses
disinfectant in Galle, Sri Lanka
"On the sides of the road, there were signs of appalling destruction: destroyed houses, ships swept to the shores by water, and trees uprooted.
"The images were grim. As you looked at the faces of people on such a day, Eid day, you could see the tragedy itself.
"There have been some efforts to ease the suffering in this region.
"Relief operations could be seen here. We were in a relief centre in a village near Galle where 500 people were killed.
"Inside the centre there were 1200 families numbering some 7500 people. All had lost their homes and were being looked after by relief agencies.
"We found the World Food Programme (WFP) doing relief work. Also present were Islamic charity associations such as Muslim Youths Association (MYA) that get financial help from different Arab countries, including Saudi Arabia.
"Arabs have offered assistance, but they were not able to make their presence more visible.
"Arabs have offered assistance, but they were not able to make their presence more visible"
"It is noteworthy that, on the way to this city, we saw a clinic flying the Israeli flag - it was sponsored by the Israeli army. They told us they had spent a week here and would spend two more. The Israelis were engaged in relief work, contrary to report we had heard that Sri Lanka had turned down offers of assistance from Israel.
"We also saw US marines, equipped with heavy machinery, removing debris and rubble from the coastal road connecting Colombo to Galle.
"There were Korean organisations too engaged in relief operations."