Pakistan’s expulsion of Save the Children is the latest turn in what has been a months-long crackdown on international aid organizations operating there, with some suspending operations in the face of Pakistani government refusal to renew their official permits.

In a news conference Friday in Islamabad, Interior Minister Chaudhry Nisar Ali Khan said Save the Children, whose international operations are based in London, “was being monitored and we have proofs and evidence” that it was “working against its agenda and charter.”

The organization’s offices were padlocked Thursday after Pakistani intelligence determined that some of its “foreign staffers” were visiting certain parts of the country, particularly in the sensitive western regions, without permission or informing relevant government agencies, an Interior Ministry official said.

“This is a violation of law and, besides, it was found that some of their activities during those visits, too, were objectionable,” said the official, who declined to elaborate. The official was not authorized to discuss the matter and spoke on the condition of anonymity.

Save the Children, which has operated for 35 years in Pakistan and has about 2,000 local employees, does not have any expatriate staffers in the country, said Michael Klosson, vice president of the organization’s U.S. branch.

“The main thing here is that this, for us, is a surprise,” Klosson said. “Suddenly, we’re being told we’re out of the business of trying to help people in Pakistan. We have this big ‘Why?’ We’re trying to seek answers; we don’t get it.”

Save the Children is one of nearly two dozen international aid organizations whose permits to operate were not renewed by the Pakistani government, beginning last fall. Some have nonetheless continued operating. Others, such as the Norwegian Rescue Council, which has a large Pakistani presence funded by European and U.N. development organizations, shut down their operations immediately but have remained in negotiations with the government.

The State Department said Friday that it was concerned about Pakistan’s “crackdown on international charitable organizations and other NGOs,” or nongovernmental organizations. It urged the government “to standardize and streamline a transparent process that will allow” such organizations, “including Save the Children, to work legally in Pakistan.”

The Pakistani government appears to be particularly concerned about what officials said were the activities of aid organizations in and near the Federally Administered Tribal Areas, where since last year the military has been conducting a major campaign against terrorist groups. In advance of the offensive, thousands of civilians were relocated, many to nearby areas also populated by refugees from decades of war in Afghanistan.

Many of the agencies, which provide health services and medical treatment among other aid, have significant operations in the tribal areas, in nearby Khyber Pakhtunkhwa province of northwest Pakistan, and in Baluchistan, the southwestern portion of the country, also bordering Afghanistan, where separatist militants and the Afghan Taliban operate.

Save the Children drew particular attention from the Islamabad government after Shakil ­Afridi, a Pakistani doctor who helped the CIA track Osama bin Laden to his hideout in the country, said during interrogation that the NGO had been instrumental in his introduction to the U.S. intelligence agency.

Afridi, who was convicted of treason and sentenced to 33 years in prison — later reduced by 10 years — said he had first met a female CIA operative in 2009 at a dinner party at the home of an expatriate Save the Children director. After performing tasks for the agency in Pakistan’s tribal regions, he conducted a fake hepatitis program in Abbottabad, the city where bin Laden was hiding, in hopes of confirming the al-Qaeda leader’s presence there.

Klosson said Save the Children had nothing to do with Afridi’s CIA recruitment and had cooperated with Pakistani investigators after the physician’s arrest. “What I recall is that we conducted an internal investigation,” Klosson said, and concluded there was no basis for claims that “we were somehow involved in recruiting Afridi.” The organization later withdrew its expatriate staff.

In recent years, Save the Children has moved to register all of its nationally based programs, in countries throughout the world, under an international organization based in London. In Pakistan, however, officials have not responded to applications Klosson said were made several years ago to change Save the Children’s registration from the U.S.-based arm to the international body.

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