There is little prospect of many refugees returning soon
A World Food Programme (WFP) spokesman told the BBC they had 400 trucks now inside Afghanistan, heading for areas where winter has already set in.
But he added that there were about six million people in urgent need of food and the WFP only had supplies for a third of that number.
The spokesman said the rapidly changing situation in the country was likely to slow down the relief work for at least a few days, but he expressed the hope that things might stabilise soon to speed up the food supplies.
Refused entry
The United Nations High Commission for Refugees (UNHCR) said that 3,000 refugees were reported to have entered northwestern Pakistan from Afghanistan on Tuesday alone.
It is urging the Alliance to refrain from committing atrocities.
Reports from the Pakistani border town of Chaman say a crowd of more than 100 refugees from Afghanistan has gathered there.
But Pakistani paramilitary forces have been preventing them from crossing over.
There are some reports of refugees returning to their villages as Taleban forces have retreated.
"We will be home for Ramadan," Habib Allah told the Associated Press news agency.
He has been living in a tent for more than a year with his relatives.
According to the UNHCR's representative in London, Claire Doole, some 2,500 Afghans have crossed back into Afghanistan from Iran over the last three days.
Mixed feelings
But there are mixed feelings about the Northern Alliance among the refugees.
Many refugees from the city of Herat, which the Alliance captured on Monday, live in the Pakistani capital, Islamabad.
"We're happy. We've been waiting for this for years, but we'll see if (the Alliance) make the same mistakes again," Omar, a carpet seller, told the French news agency AFP.
Fazul Rahim Ansari said he would go back to Herat as soon as possible.
"We're all happy now. With the help of God, these guys (the Northern Alliance) won't fight against each other," he said.
But social worker Rahima Delir is more cautious.
"We'll see if there will be peace, then we'll go back," she told AFP. "We don't trust that there's peace yet."
The UNHCR estimates some 135,000 Afghans have fled into Pakistan since the 11 September terror attacks on the United States.
That is still a small number compared to the millions of Afghans who left to live in Pakistan and Iran during the years of fighting in Afghanistan.