The administration on Saturday ordered all local and foreign non-governmental organisations (NGOs) not to let female staff work until further notice. It said the move, which was condemned globally, was justified because some women had not adhered to the Taliban's interpretation of Islamic dress code for women.
Three NGOs - Save the Children, Norwegian Refugee Council and CARE International - said in a joint statement that they were suspending their programmes as they awaited clarity on the administration's order.
"We cannot effectively reach children, women and men in desperate need in Afghanistan without our female staff," the statement said, adding that, without women driving the effort, they would not have reached millions of Afghans in need since August last year.
Separately, the International Rescue Committee (IRC) said in a statement that it was suspending its services in the country, citing similar reasons. IRC said it employs more than 8,000 people in Afghanistan, over 3,000 of whom are women.
The suspension of some aid programmes that millions of Afghans access comes at a time when more than half the population relies on humanitarian aid, according to aid agencies, and during the mountainous nation's coldest season.
Save the Children, Norwegian Refugee Council and CARE International also highlighted the effect of the ban on female staff on thousands more jobs in the midst of an economic crisis.
Earlier, international aid agency AfghanAid said it was immediately suspending operations while it consulted with other organisations, and that other NGOs were taking similar actions.
The International Committee of the Red Cross in Afghanistan also on Sunday expressed concern at the move and an earlier bar on women from attending university, warning of "catastrophic humanitarian consequences in the short to long term".
'Obliged to comply'
A spokesman for the Taliban administration, Zabihullah Mujahid, hit back at the criticism, saying all institutions wanting to operate in Afghanistan are obliged to comply with the rules of the country.
"We do not allow anyone to talk rubbish or make threats regarding the decisions of our leaders under the title of humanitarian aid," Mujahid said in a post on Twitter, referring to a statement by the head of U.S. Mission to Afghanistan.
Chargé d'Affaires Karen Decker had taken to Twitter to question how the Taliban planned to prevent hunger among women and children following the ban. She pointed out that the United States was the largest humanitarian aid donor to the country.