WASHINGTON — US officials believe Pakistan's spy agency was behind the killing of a Pakistani journalist who reported that Islamist militants had infiltrated the military, the New York Times reported.

The newspaper quoted two senior officials as saying that intelligence showed that senior members of Pakistan's powerful Inter-Services Intelligence (ISI) agency ordered the killing of Saleem Shahzad, 40, to muzzle criticism.

The report was likely to further raise tensions between the uneasy allies following the US commando raid north of Islamabad in May that killed Al-Qaeda chief Osama bin Laden and was carried out without Pakistan's knowledge.

One of the US officials quoted by the Times described the actions of the ISI -- which has historic ties to Islamist militants in neighboring Afghanistan and disputed Kashmir -- as "barbaric and unacceptable."

It quoted another senior official as saying: "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."

The ISI has denied as "baseless" allegations that it was involved in the murder of Shahzad.

The reporter, who worked for an Italian news agency and a Hong Kong-registered news site, went missing en route to a television talk show and his body was found last week south of the capital, bearing marks of torture.

A senior South Asia researcher at Human Rights Watch, Ali Dayan Hasan, said that the 40-year-old had recently complained of threats from the ISI, adding: "In the past the ISI has been involved in similar incidents."

Shahzad disappeared two days after writing an investigative report in Asia Times Online saying Al-Qaeda carried out a recent attack on a naval air base to avenge the arrest of naval officials held on suspicion of Al-Qaeda links.

An ISI official said last week that Shahzad's "unfortunate and tragic" death was a "source of concern for the entire nation" but "should not be used to target and malign the country's security agencies".

The government has ordered an inquiry into the kidnapping and murder, pledging that the culprits would be brought to justice, but angry journalists say past investigations into killings of journalists have come to nothing.