Aid agencies fear that not enough food will be delivered
Ms Short has rejected calls for a halt to bombing as unreal and emotional, saying such a move was not "a real alternative".
The only way to avert a humanitarian crisis was to drive the Taleban from power, she said.
But a spokeswoman for the charity Oxfam International said Ms Short's comments were a "cheap shot".
Ms Short, at the end of a trip to Pakistan, said: "I met local representatives of all these agencies, as opposed to their spin-doctors ... I asked each one whether they knew of their delivery systems inside Afghanistan and most of the agencies said 'yes the distribution networks are holding up'."
But the Oxfam spokeswoman said: "I don't know who she has been speaking to but I have spoken to our people in the area and we have not got enough food to deliver."
Ms Short later told the Guardian newspaper that stopping the military action was not a "real alternative, it's emotional".
Weather worry
She went on to suggest that as each area of Afghanistan was made safe, international aid could be moved in.
"I imagine a set of virtuous dominoes.
"Area after area where it becomes safe to move, international staff return, the humanitarian operation becomes more successful and then ideally with a new Afghan government whose authority is extended bit by bit."
But a spokesman for Christian Aid warned some areas of Afghanistan would soon be cut off by snow.
"We need to get 70,000 tonnes to them in the next few weeks and we are not going to be able to do that.
"The lorry drivers are scared of driving slow, heavy trucks in a war zone, and understandably so - mistakes do and will happen," he told the Times.