Pakistan has ordered all Save the Children's foreign staff to leave the country within four weeks after allegations linking the aid agency to a fake vaccination programme used in the hunt for Osama bin Laden.
Save the Children said it had received no explanation for the order, under which the charity's six expatriate staff have been told to leave within four weeks.
But a Pakistan intelligence report has linked the aid agency to Pakistani doctor Shakeel Afridi who the CIA allegedly used to carry out a fake vaccination programme as they searched for the Al-Qaeda chief.
"Earlier this week we got a call from special branch instructing us to send back all expatriate staff," Save the Children spokesman Ghulam Qadir said.
"There were no reasons given. We are working with the government to comply with the instructions."
He said the agency would continue to operate in Pakistan where it has 2,000 staff, serving more than seven million children.
And he strongly denied allegations that Afridi was introduced to the CIA through Save the Children.
"On Shakeel Afridi, our stand is very clear that there is absolutely no truth in it. There is no concrete proof to these allegations," Qadir said.
No Pakistani government official was immediately available to comment.
But the US State Department said it strongly supported the work of Save the Children in Pakistan.
"We are deeply concerned and have raised this issue with the government of Pakistan and urged it to allow Save the Children to continue its important work," said acting deputy spokesman Patrick Ventrell.
"Independent NGOs are among the essential building blocks of any healthy democracy. So in Pakistan, as in other countries, we urge governments to help create an environment in which they can operate productively."
Richard Hoagland, the US deputy ambassador to Pakistan, also denied that Save the Children had anything to do with the discovery of bin Laden, who was living in the garrison town of Abbottabad, north of Islamabad.
"Save the Children' were in no way involved with Abbottabad -- I repeat, no way. A very sad and misguided over-reaction," he wrote on Twitter.
Afridi allegedly worked for the CIA collecting DNA in a bid to verify bin Laden's presence in the town, where US Navy SEALS killed the Al-Qaeda leader in a raid on his compound in May 2011.
Pakistan reacted with fury to the raid, which it branded a violation of sovereignty.
An official report prepared jointly by Pakistan civil and military intelligence blamed a former Save the Children director for introducing Afridi to the Americans.
The report, obtained by AFP, said Afridi went to Peshawar in November 2008 to participate in a workshop organised by Save The Children, where he met the charity's country director, who later invited him to come to Islamabad.
Afridi met him at a book stall in Islamabad and was introduced to a western woman, the report said. Afridi and the woman met regularly afterwards in various locations in the capital.
In May Afridi was sentenced to 33 years in jail for treason after being convicted over alleged ties to militant group Lashkar-e-Islam, not for working for the CIA, for which the court said it did not have jurisdiction.
The United States was enraged by Afridi's sentencing and the Senate Appropriations Committee voted to cut aid to Pakistan by a symbolic $33 million.