By Staff Reporter
Police have sealed off their offices in Islamabad and foreign staff given 15 days to leave the country.
Save the Children said it “strongly objected” to the action.
The charity has always denied being involved with the CIA or Pakistani doctor Shakil Afridi, who carried out the programme.
The charity has had no foreign staff in the country for the past 18 months in response to the accusations.
It now has 1,200 Pakistani staff working on projects in health, education and food, the charity said.
Save the Children, which has operations all over the world, has worked in Pakistan for more than 30 years.
No government explanation
The Pakistani government has not given a formal announcement explaining the decision.
But one official told the AFP news agency: “Their activities were being monitored since a long time. They were doing something which was against Pakistan’s interest.”
A police official said that the charity’s phone calls and offices had been placed under surveillance. Speaking to the Reuters news agency, he added that the charity’s activities were “very suspicious”.
Condemning the move, Save the Children said it was “raising our serious concerns at the highest levels”, adding that its workers were all Pakistani nationals.
A Save the Children official told Reuters that the Pakistan government had been stopping aid shipments entering the country, “blocking aid to millions of children and their families”.
It comes after the Pakistani government announced it was tightening the rules for NGOs, revoking several of their licences.
The BBC understands that one of those NGO’s, the Norwegian Refugee Council, has ceased all operations in Pakistan as its licence has not yet been renewed.