The USS Abraham Lincoln provided crucial support post-tsunami
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The US aircraft carrier which despatched the first helicopters to deliver aid to Aceh after the tsunami has left the area.
"The mission has been accomplished," a spokesman for the US embassy in Jakarta said.
Australian troops will also be leaving Aceh in the next few weeks, said Prime Minister John Howard.
The Indonesian government has indicated it would like to be in control of the aid operation by the end of next month.
Indonesia has so far buried 111,171 people who died in the 26 December tsunami, while more than 127,000 others remain missing, the government said on Thursday.
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We're more than capable of providing the kind of help needed by these kind of communities, with or without Abraham Lincoln
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Many thousands more have been left homeless.
Indonesian Social Welfare Minister Alwi Shihab and military chief General Enriartono Sutarto bid farewell to some 1,000 servicemen on the deck of USS Abraham Lincoln.
"I hope this [mission] will pave the way for a wider range of co-operation between our two armed forces," Mr Sutarto said.
The decision to remove the aircraft carrier was taken because the Indonesian authorities "believe they have the facilities between them and the UN and other NGOs to do the job", a spokesman for the US embassy in Jakarta said.
A local aid spokesman for the International Rescue Committee in Aceh, Greg Beals, was relaxed about the aircraft carrier's withdrawal.
"We're more than capable of providing the kind of help needed by these kind of communities, with or without Abraham Lincoln... at this point, we're pretty much all set," he said.
He said the focus of the aid operation was beginning to switch to longer-term requirements such as housing.
The US is also deploying Mercy, a floating hospital, and USS Essex, a smaller aircraft carrier.
Australian withdrawal
In addition, Japan, Germany, and Australia all have a military presence in Aceh.
However, Australia, too, is expected to withdraw its military support from Aceh in the near future.
Mr Howard, speaking to reporters in Singapore following his tour of damage to Aceh on Wednesday, said: "I think you're looking at weeks rather than months [as a timeframe]."
Australia is one of the largest donors to tsunami-affected areas, having pledged A$1bn ($773m) to relief efforts in Indonesia.
Mr Shihab said on Wednesday that Jakarta hoped it could handle the welfare mission without foreign troops by the end of March.
"By 26 March we will be able to stand on our own feet," he told a news conference in Banda Aceh.
He said Indonesian boats would take the role played so far by foreign helicopters of reaching isolated communities to bring them goods and services.
He said the emergency stage of the aid operation was now over, and attention was turning to reconstruction and rehabilitation.
Barracks would be used to house the homeless - 374 of these would be built by 15 February and a similar amount by the end of the month, he said.
Mr Shihab said the authorities would start cataloguing refugees' skills in order to allocate them reconstruction work. The Indonesian military is particularly keen to see foreign troops leave Aceh. It has been involved in a long-running war against separatist rebels in the province, and does not want the international community to get involved.
Indonesian officials and the leadership of the Free Aceh Movement (Gam) held talks in Helsinki last week in an attempt to restart a peace process but the discussions ended only with an agreement to meet again, probably later this month.