The International Committee of the Red Cross (ICRC) has suspended humanitarian activities in two of Pakistan's largest cities, Peshawar and Karachi.
The move follows the killing of Khalil Dale, a British nurse working for the group.
His beheaded body was found on 29 April, after he was abducted four months ago.
Humanitarian groups say they are reviewing their presence in Pakistan because of increased attacks on staff.
"The recent attack against the ICRC compels us to completely reassess the balance between the humanitarian impact of our activities and the risks faced by our staff," said Jacques de Maio, ICRC's head of operations for South Asia.
Paul Castella, head of the ICRC delegation in Pakistan, said that in the coming weeks the organisation would announce a decision on its future presence in Pakistan.
The organisation has already stopped its activities in the south-western province of Balochistan and its capital, Quetta, where Mr Dale's body was found.
A note found beside the body blamed the organisation for failing to pay a ransom.
Thursday's announcement means the ICRC is not currently operating in three of Pakistan's four provinces.
On Wednesday, a statement from the Pakistan Humanitarian Forum (PHF) - an umbrella group of nearly 50 charities - warned that recent murders and kidnappings of international aid workers would further impede efforts to help the most vulnerable in Pakistan's conflict areas.
According to PHF, at least 19 aid workers have been murdered across Pakistan since 2009. More than 20 were abducted by militants and criminals.
It has warned that "this trend of increased targeting of humanitarian aid organisations and personnel will further impede the ability of humanitarian agencies to provide life-saving and life-enhancing support to the most vulnerable population".
Some groups have warned that if the increasing targeting of humanitarian agencies continues, aid workers will have no choice but to withdraw from the most risky areas - that would leave millions of displaced and suffering Pakistanis with virtually no-one to turn to, BBC correspondents say.
Pakistan relies heavily on aid organisations - some of them, like the ICRC, have been operating in the country since 1947.
Earlier this week, US hostage Warren Weinstein appeared on a video posted on Islamist websites, pleading with US President Barack Obama to meet his captors' demands.
Mr Weinstein, 70, an aid expert living in Pakistan, was kidnapped by armed men in the city of Lahore last August.