The charity's country office here was sealed yesterday after government officials accompanied by police placed a lock on its gate and and asked employees to leave.
The non-governmental organisation's foreign staff has been directed to leave Pakistan within 15 days, police said.
A statement issued by the Interior Ministry said the international NGO was involved in "anti-Pakistan activities", Geo News reported.
Interior Minister Chaudhry Nisar Ali Khan said NGOs working against the country's national interest will not be allowed to continue its work in Pakistan.
The interior minister added that they had been receiving intelligence reports for many years but no action was being taken. NGOs, whose numbers run into hundreds, have been operating without any code of conduct, law and agenda, he said.
He also appealed to all international NGOs and governments to respect the laws of Pakistan, adding that the government will not bear any kind of foreign pressure regarding the working criteria of the NGOs.
"Save the Children was not served any notice to this effect. We strongly object to this action and are raising our serious concerns at the highest levels," it said.
The NGO added that it has been operating in Pakistan for over 35 years and that currently it had 1,200 employees in the country but none of them a foreign national.
Pakistan has previously linked the charity to the fake vaccination programme used by the CIA to track down al-Qaeda chief Osama Bin Laden.
The NGOs activities had been under strict scrutiny for the past six months.
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