Most foreign aid workers, including all UN expatriate staff, left Afghanistan last week for security reasons. But the agencies said they were still able to provide some food and other services inside the country through Afghan nationals who continued to operate the programmes in their absence.
No more food can now be delivered and the World Food Programme predicts that reserve supplies will be exhausted in two to three weeks.
The agencies offered special thanks to Pakistan and Iran, neighbouring nations that together have taken in some 3.5 million Afghans in recent years - refugees fleeing decades of war, three years of severe drought and a collapsed economy.
They appealed to the international community for help in paying for and carrying out efforts to supply food, water, medical and sanitation supplies, tents and other emergency goods.
In the Pakistan capital, Islamabad, World Food Programme spokesman Khaled Mansour said the Taleban moves threatened to "disrupt, if not completely stop, our food distribution".
UN spokeswoman Stephanie Bunker said about 700 Afghan staffers had carried on with much of the world body's work since last week's departure of foreign workers, but that activity too now appeared to have stopped.
She said the UN office in Kandahar had been seized and the Taleban had also taken over some offices of non-governmental organisations that provide relief services.
Communications equipment had been shut down in both Kandahar and Kabul.
- REUTERS
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