US officials say they have intelligence that Pakistan’s powerful spy agency ISI ordered the killing of a Pakistani journalist who had written scathing reports about Islamist militants having infiltrated into the country’s military.

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, “New York Times” reported quoting two senior Obama administration officials.

The intelligence, administration officials said they believed was reliable and conclusive, showed that the actions of the ISI, as it is known, were “barbaric and unacceptable”.

But the disclosure of the information could further aggravate the badly fractured relationship between the US and Pakistan, which worsened significantly with the American commando raid two months ago that killed Osama bin Laden in a Pakistan safehouse.

The newspaper said Obama administration officials will deliberate in the coming days how to present the information about Shahzad to the Pakistani government, an 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 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.

A spokesman for the Pakistan intelligence agency said in Islamabad yesterday that, “I am not commenting on this.”

George Little, a spokesman for the Central Intelligence Agency, declined to comment.

In a statement the day after Shahzad’s waterlogged body was retrieved from a canal 60 miles from Islamabad, the ISI publicly denied accusations in the Pakistani news media that it had been responsible, calling them “totally unfounded.”

The ISI said the journalist’s death was “unfortunate and tragic,” and should not be “used to target and malign the country’s security agency.”

The killing of Shahzad, a contributor to the Web site Asia Times Online, aroused an immediate furor in the freewheeling news media in Pakistan.

Shahzad was the 37th journalist killed in Pakistan since the 9/11 attacks, according to the Committee to Protect Journalists.

Pakistan's civilian government, under pressure from the media, established a commission headed by a Supreme Court justice to investigate his death. The findings are scheduled to be released early next month.

The journalist suffered 17 lacerated wounds delivered by a blunt instrument, a ruptured liver and two broken ribs, said Dr Mohammed Farrukh Kamal, one of the three physicians who conducted the post-mortem.

The anger over Shahzad’s death followed unprecedented questioning in the media about the professionalism of the Army and the ISI, a military-controlled spy agency, in the aftermath of the Bin Laden raid.

Since that initial volley of questioning, the ISI has mounted a steady counter-campaign. Senior ISI officials have called and visited journalists, warning them to douse their criticisms and rally around the theme of a united country, according to three journalists who declined to be named for fear of reprisals.

Shahzad, who wrote articles over the last several years that illuminated the relationship between the militants and the military, was abducted from the capital three days after publication of his article that said Al Qaeda was responsible for an audacious 16-hour commando attack on Pakistan’s main naval base in Karachi on May 22.

The attack was a reprisal for the navy's arresting up to 10 naval personnel who had belonged to a Qaeda cell, Shahzad said.

The article, published by Asia Times Online, detailed how the attackers were guided by maps and logistical information provided from personnel inside the base.

Particularly embarrassing for the military, Shahzad described negotiations before the raid between the navy and Al Qaeda representative, Abdul Samad Mansoor.

The navy refused to release the detainees, Shahzad wrote. The Pakistani military maintains that it does not negotiate with militants.