Saleem Shahzad had complained of ISI threats Pakistan “sanctioned” the killing of journalist Saleem Shahzad, the highest-ranking officer in the US military, Admiral Mike Mullen, has said.
But he said he could not confirm if the country’s powerful intelligence agency, the ISI, was involved.
The Pakistani government called the statement “extremely irresponsible”. The ISI has denied any involvement.
Mr Shahzad was kidnapped near his home in Islamabad in May. His body was found two days later in Punjab province.
At the time, many in the Pakistani media blamed the Pakistani intelligence agency for the murder, despite its denial.
An inquiry set up by the government to investigate the killing began work last month.
“I have not seen anything that would disabuse that report that the government knew about this,” Adm Mullen told journalists in Washington on Thursday.
“It was sanctioned by the government, yeah,” he said.
Adm Mullen added that he did not have a “string of evidence” linking the death to the ISI.Downward spiral
Pakistan had set up an independent commission into the killing and Adm Mullen’s statement would not help that investigation, a government spokesman said. This point was repeated by Husain Haqqani, Pakistan’s ambassador to the US.
“Any evidence that our American friends have should be shared with that commission,” Mr Haqqani told the New York Times newspaper.
“We are as interested in getting to the bottom of this matter as anyone else in the world, given our concern about human rights,” he said.
Nevertheless, correspondents say, the remarks will further worsen ties between Washington and its ally, Islamabad.
The relationship has been on a downward spiral for many months. Tensions worsened after the killing of al-Qaeda leader Osama Bin Laden by US commandos in the Pakistani city of Abbottabad.
Last month Adm Mullen publicly acknowledged that there would be substantial cuts to US military numbers in Pakistan.
He said that US-Pakistan ties needed time to heal but added that it would be dangerous to abandon Islamabad.
“I think the worst thing we could do would be cut them off,” he said. If that happened, he said, “10 years from now, 20 years from now, we go back and it’s much more intense and it’s much more dangerous”.
Adm Mullen steps down as chairman of the Joint Chiefs of Staff later this year.Journalist ‘danger’
Mr Shahzad, who worked for the Hong Kong-based Asia Times Online and the Italian news agency Adnkronos International, had made a career writing about various Islamist militant networks operating in Pakistan.
Shortly before his death he had written an article about al-Qaeda infiltration in Pakistan’s navy.
He reported that the militant group was behind a recent deadly assault on the Mehran base in Karachi because talks had failed over the release of several naval personnel arrested on suspicion of links to al-Qaeda affiliates.
Human rights groups have called Pakistan the most dangerous place in the world for journalists to operate, saying they were under threat from Islamist militants but also Pakistan’s military and intelligence agencies.