Afghan Taliban banned WHO and the Red Cross activities for what they said were "suspicious" actions during vaccination campaigns, as polio is still crippling the country.
The International Committee of the Red Cross (ICRC) said on Thursday it had suspended work in Afghanistan after the Taliban announced a "ban" against the humanitarian group and the World Health Organization.
According to a Taliban statement on Thursday, the ICRC had not "acted upon its agreements" with the Taliban.
The insurgents, who control or influence about half of Afghanistan, also accused the WHO of "suspicious movements" during a vaccination campaign.
The move comes as the WHO is carrying out a vaccination campaign in Afghanistan, one of the last countries in the world where polio is still endemic.
Taliban spokesman Zabihullah Mujahid said fighting across Afghanistan had created a "complex situation" and some charitable organisations including the WHO and the Red Cross were not operating in accordance with the situation.
As a result, campaigns to vaccinate children against the crippling polio virus have often hit obstacles with workers coming under attack or being "banned".
"They have not stuck to the commitments they had with the Islamic Emirates, and they are acting suspiciously during vaccination campaigns," he said, providing no details.
Other aid groups were free to continue operations, he said.
Aid groups and vaccination campaigns have often been the target of suspicion and violence in both Afghanistan and Pakistan. Hardline groups and militants often accuse the West of trying to sterilise the Muslim populations or spy on them under the pretext of health care.
ICRC spokesman Robin Waudo said the organisation had put its activities on hold in war-torn Afghanistan, where many in rural areas have scant access to health care and where polio rates are rising.
"We acknowledge this announcement and have suspended our activities in the country due to the withdrawal of security guarantees," said Waudo.
"Therefore, we are now in the process of contacting the [Taliban] to initiate a bilateral and confidential dialogue in view of the statement," he said.
The WHO did not immediately respond to requests for comment.