The New York Times reports:

Obama administration officials believe that Pakistan’s powerful spy agency ordered the killing of a Pakistani journalist who had written scathing reports about the infiltration of militants in the country’s military, according to American officials.

New classified intelligence obtained before the May 29 disappearance of the journalist, Saleem Shahzad, 40, from the capital, Islamabad, and after the discovery of his mortally wounded body, showed that senior officials of the spy agency, the Directorate for Inter-Services Intelligence, directed the attack on him in an effort to silence criticism, two senior administration officials said.

The intelligence, which several administration officials said they believed was reliable and conclusive, showed that the actions of the ISI, as it is known, were “barbaric and unacceptable,” one of the officials said. They would not disclose further details about the intelligence.

But the disclosure of the information in itself could further aggravate the badly fractured relationship between the United States and Pakistan, which worsened significantly with the American commando raid two months ago that killed Osama bin Laden in a Pakistan safehouse and deeply embarrassed the Pakistani government, military and intelligence hierarchy. Obama administration officials will deliberate in the coming days how to present the information about Mr. Shahzad to the Pakistani government, an administration official said.

The disclosure of the intelligence was made in answer to questions about the possibility of its existence, and was reluctantly confirmed by the two officials. “There is a lot of high-level concern about the murder; no one is too busy not to look at this,” said one.

A third senior American official said there was enough other intelligence and indicators immediately after Mr. Shahzad’s death for the Americans to conclude that the ISI had ordered him killed.

“Every indication is that this was a deliberate, targeted killing that was most likely meant to send shock waves through Pakistan’s journalist community and civil society,” said the official, who like others spoke on the condition of anonymity because of the delicate nature of the information.