“It was sanctioned by the government,” Mullen told journalists at the Pentagon on Thursday. “I have not seen anything to disabuse the report that the government knew about this.”

Mullen’s comments are the first high-level confirmation that Washington believes its nominal allies in Islamabad ordered the kidnapping, torture, and killing of Syed Saleem Shahzad, 41, in May. The comments will only add new stress to the deeply troubled relationship between the two countries. Many members of Congress from both parties have been calling for the United States to reevaluate—and possibly cut—its extensive financial aid to Pakistan amid growing questions about Pakistan’s willingness to combat the militants who operate out of extensive safe havens within its own borders.

Mullen said he couldn’t confirm press reports that Pakistan’s powerful Inter-Services Intelligence agency had carried out Shahzad’s murder. An array of U.S. military and intelligence officials believe the ISI killed Shahzad to prevent him from continuing a series of investigative articles about the infiltration of militants from al-Qaida and other extremist groups into Pakistan’s military and intelligence services.