The charity office in Islamabad was found locked on Thursday evening (June 11) and police had posted a notice that said the building had been sealed.
A Pakistani senior police official said, "We have been monitoring their calls and watching their offices and their activities are very suspicious.”
Save the Children denied the allegations and voiced concern that millions of children would be blocked from receiving aid.
"We strongly object to this action and are raising our serious concerns at the highest levels," the agency said in a statement.
"All our work is designed and delivered in close collaboration with the government ministries across the country and aims to strengthen public service delivery systems in health, nutrition, education and child welfare.”
Additionally, Save the Children employees said the government has denied several staff members visas since 2012.
Publication date: June 12, 2015