ISLAMABAD—Pakistan’s interior minister warned international nongovernmental organizations Friday that they won't be allowed to operate “against national interests,” a day after authorities ordered the charity Save the Children to shut down its operations in the country and sealed its main office.

Pakistani Minister of Interior Chaudhry Nisar Ali Khan said the government had evidence that Save the Children Pakistan, part of the U.K.-based Save the Children International network, had been “working contrary to its charter and agenda for years” in Pakistan.

Pakistani authorities have said in the past they suspect NGOs are being used to conduct espionage, while some religious leaders have criticized them for conveying Western values and culture.

“My message to international NGOs and other governments is that we welcome the NGOs doing good work, but they will have to respect Pakistani law and regulations,” said Mr. Khan. “They will have to respect Pakistan’s national interest.”

Mr. Khan declined to offer details about the evidence he said the government has against Save the Children.