An estimated 18 million Afghans are in need of humanitarian assistance and more than three million children are at risk of acute malnutrition.
Concern CEO Dominic MacSorley said the focus must be put back on the millions of people who will not get on a flight and may never cross a border.
Many aid organisations are continuing to maintain a presence in Afghanistan to assist in charitable programmes.
Speaking on RTÉ's Morning Ireland programme, Mr MacSorley said there is a greater need than ever for the United Nations, NGOs and diplomats to stay in the country as the US military withdraws, saying there is a huge fear that Afghanistan is going to slip into isolation which would be "disastrous".
Concern staff in Afghanistan are "cautiously back at work" but there is a huge amount of fear and anxiety, he said.
There are around 200 Concern staff members in Afghanistan and 30 are women.
Mr MacSorley said the Taliban gave assurances that NGOs can continue their work.
He said the female staff members are continuing to work - some at home and some in the office - and negotiations are ongoing to see if they can return to the communities, because the level of freedom for women is still unknown and still being worked on.
Before this latest challenge in the country, he said the humanitarian assistance appeal was only 38% funded - a shortfall of €800 million.
He called for international donors to step up, saying that billions had been spent on a failed military operation.
Mr MacSorley said the population of Afghanistan is already on its knees from a humanitarian perspective and things are only going to get worse.