Assistant Immigration Minister Matt Thistlethwaite confirmed 41 Australians remain unaccounted for on Saturday morning, after a landslide of ice and rock burst the banks of the Trishuli River.
Chinese and Nepalese authorities warn further flooding may occur, complicating rescue efforts and posing a risk to communities in the area.
At least 579 people in Nepal and five in China's Tibet are dead, with the number missing in Nepal nearly doubling to 1924, the country's disaster authority said on Friday.
More than 550 were unaccounted for in Tibet's Gyirong County, including 260 foreigners, according to Chinese state broadcaster CCTV.
Mr Thistlethwaite told ABC News Breakfast DFAT staff were in Kathmandu making contact with as many Australians as possible.
He said families were desperate for news about loved ones
"There was quite a bit of despair and anxiety in (the) community; we're doing our best to support the Tibetan and Nepalese communities here in Australia," Mr Thistlethwaite said.
At least 10,000 homes have been destroyed, with many roads cut off due to the extensive damage by the floods, he said.
"There's no telecommunications infrastructure to the region. Power's been cut off. So our DFAT officials are getting as close as they possibly can to the region."
Nepal has accepted a $5 million humanitarian aid package from Australia.
Several Australians with family in the affected region have flown to assist the search for survivors, combing towns inundated by debris and mud.
Among them is the husband of NSW mother-of-two Reshma Patel, who was due to touch down in Kathmandu on Friday evening.
Like the majority of the Australians confirmed missing, Ms Patel was making a pilgrimage with a tour group when the floods began.
Her last known location was an immigration office along the Nepal-Tibet border, which was captured on viral footage.
"She was inside the big building, which you can see in all the videos that had been hit hard by the floods at the border," family friend Chin Valsan told AAP.
"After that, there is no contact whatsoever."
Ms Patel had been travelling with the Isha Foundation for almost two weeks and was due to fly home to Sydney from Kathmandu on Thursday.
"That hasn't happened," Mr Valsan said.
While search and rescue operations, aided by Australian officials, are ongoing, charities have banded together nationally to raise funds.
The Nepal Flood Disaster Appeal has been established by a coalition of 15 organisations including Oxfam Australia and Save the Children Australia.
The group, known as the Emergency Action Alliance, warns survivors may find themselves cut off from reliable shelter, food, drinking water and medical care.
It is a fear shared by Kiran Thapa, 46, who told AAP his family in Nepal had survived the floods but the real "trauma" would come once the dust had settled.
The paddy fields his family relies on for food had been destroyed while he worried his elderly mother may not have access to medication.
"After a few weeks or so, when they come to the realisation they've lost everything ... that may be very hard for them to digest," he said.
The Australian Red Cross has announced all donations to its global emergency fund from Thursday would go to Nepal, while World Vision Australia has launched a dedicated appeal.
UNICEF is appealing for $US17.2 million to fund its emergency relief and recovery efforts, including for the estimated 17,000 children affected.
Impacting recovery efforts are fears of possible further flooding, which reportedly delayed a Chinese rescue operation on Friday.
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