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The Christian charities World Vision and Catholic Relief Services are among 18 organisations expelled from Pakistan.
They had been accused of "deliberately spreading disinformation" and "non-compliance" by the country's government - which did not give more details.
In a statement seen by Premier, World Vision said it had handed over responsibility for its poverty-reduction and health programmes to the state and had compiled with a 60-day deadline to leave.
It continued: "World Vision regrets the effect that the cessation of our work will have on the vulnerable communities with whom we worked, but respects the Government's right to decide who may work in the country."
Its expulsion follows a two-year battle by World Vision to formally register in Pakistan. The charity had been appealing a decision in December 2017 not to grant registration.
Absolutely incorrect - INGOs denied registration delib spreading disinfo. 80 plus re-registered. 18 denied for non compliance viz what they had defined as their work. They must leave. They need to work within their stated intent which these 18 didn't do! https://t.co/qgvpWfXpQP— Shireen Mazari (@ShireenMazari1) December 5, 2018
World Vision was employing in Pakistan 31 members of staff - using funding from Canada and the US.
The international organisation first began operating in Pakistan 13 years ago. Since 2015, it says it has helped 800,000 youngsters.
The statement continued: "[World Vision] will continue to discuss the possibility of re-starting work under any new legal framework which the government may subsequently introduce."
In a message published on Twitter, Pakistan's Human Rights Minister Shireen Mazari referred to the 18 organisations, saying: "They must leave.
"They [international non-government organisations] need to work within their stated intent which these 18 didn't do."
Catholic Relief Services, which is a charitable arm of the US Catholic Church, had been helping provide access to food, education and clean water in Pakistan since 1954.
There is speculation the expulsions are partly motivated by Pakistan's anger at a US-led covert operation which identified the home of Osama bin Laden in 2011.
Islamabad says the United States never gave advance notice of a night-time raid by Navy Seals in Abbottabad which saw the founder of al-Qaeda killed. Pakistan perceived the operation as an invasion of its sovereignty.
The sting involved a Pakistani doctor posing as an international aid worker promoting a vaccination program to try to get DNA samples from bin Laden's family to help identify his whereabouts.
Michael Kugelman, deputy director of the Asia Programs at the Washington-based Wilson Centre, told Associated Press: "It's hard to overstate the significance of the hunt for bin Laden and the impact it had on Pakistani perceptions of foreign NGOs."
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