World Vision Australia's Patrick Thomas told an inquiry into Australia's engagement in Afghanistan on Wednesday that the organisation was paying administration fees of around seven per cent through informal networks due to a crisis in the country's banking system.
"We've been able to get the majority of that money into country but via the hawala network which comes at great cost to us," said Mr Thomas, referring to the money broker system.
"At the moment that is the price of doing business in a way, but it's unacceptable as a humanitarian organisation when the need is so great on the ground to be slugged those fees."
The fee rate to use the hawala system has been rising rapidly, the Senate committee was told, and there are concerns over its lack of transparency.
The Taliban surged back to power in Afghanistan in September after two decades of fighting against US-led coalition forces which included Australian defence personnel.
The swift change of regime in Kabul has prompted an unprecedented number of visa applications from individuals seeking resettlement.
Many governments and organisations have frozen assets and funding to Afghanistan, a move intended to halt the flow of money to the Taliban, though the decision risks harming the general population.
Afghanistan is grappling with a liquidity squeeze - lack of available money - which means there are strict limits on the amount of cash that residents and businesses can withdraw.
The UN is importing some hard currency that businesses and organisations may be able to access in Afghanistan, though the amounts remain modest compared to the high demand for cash, the committee was told.
Australia does not recognise or have formal diplomatic relations with the Taliban, although it engages with the regime on some matters such as humanitarian assistance and safe passage for those trying to leave.
Mat Tinkler, acting chief executive of Save The Children Australia, told the hearing there were more than 13 million children in need of help.
"It's hard to believe that a living hell could get worse, but it did," Mr Tinkler told the committee.
The Afghan people are facing drought conditions that are affecting food supplies, as well as dealing with the country's general economic malaise and fallout from the conflict and regime change.
Daniel Sloper, special representative for Afghanistan at the Department of Foreign Affairs and Trade, told the committee the international community was cautious to make sure health funding being channelled into Afghanistan did not benefit the Taliban.
The Australian government announced last year it would contribute $100 million in humanitarian assistance for the people of Afghanistan, though getting support directly to at-risk people remains a challenge for governments around the world.
Australia has so far disbursed $22.5 million to international partner organisations working in Afghanistan, the committee was told.
In an interim report published in January, the bipartisan committee said the government should reveal the full cost of Australia's involvement in the Afghanistan mission and that it do more to resettle those displaced by years of war.
The government in January announced it would allocate 15,000 humanitarian and family visa places to Afghan nationals over the next four years.
Refugee and religious groups have said the measure is insufficient as they are seeking a large increase in Australia's overall humanitarian intake to accommodate those displaced.
