Pakistan has lashed out at America's top-ranking military officer, Admiral Mike Mullen, on Friday, saying that its relations with the US have been further damaged by his remarks blaming the Islamabad government for the killing, torture and murder of a Pakistani journalist.

The chairman of the joint chiefs of staff shocked Islamabad by saying publicly what US officials had confirmed only in private: that the Pakistani government had "sanctioned" the killing of Syed Saleem Shahzad, the investigative reporter for Asia Times Online whose mutilated body was found on 30 May in a canal 40 miles from the capital. He had been writing about jihadist infiltration of the Pakistani military.

Pakistan's information minister, Firdous Ashiq Awan, told a news conference Mullen had made an "extremely irresponsible and unfortunate statement".

"This statement will create problems and difficulties for the bilateral relations between Pakistan and America. It will definitely deal a blow to our common efforts with regard to the war on terror," she said, without going into details.

The row comes at a time when ties between the two countries have not recovered from the US raid that killed Osama bin Laden on 2 May in the central Pakistani town of Abbottabad. Pakistan's armed forces are smarting from the humiliation of the special forces mission, which was carried out without their permission or knowledge. After discovering the al-Qaida leader near a military academy in a town full of retired officers, the US remains suspicious that he had been helped by members of the Pakistani government, army or the Inter-Services Intelligence spy agency.

Since the raid, Islamabad announced it was stopping US drone flights launched from its soil, although US officials said the flights, aimed at tracking down and killing al-Qaida members and other militants, had been suspended in April, after a row over Islamabad's arrest of a CIA contractor, Raymond Davis, who shot two Pakistani nationals in Lahore in January.

It is unclear whether Mullen's remarks were approved beforehand by the White House or whether they simply reflected the frustration of a senior officer approaching retirement in two months, who invested considerable time in cultivating relationships with his Pakistani counterparts.

US and British intelligence officials believe that apart from a small department dealing with foreign agencies, the ISI's conduct is beyond the influence of the civilian government in Islamabad and its western allies.

Washington and London are anxious the poor human rights record of the Pakistani security services may have helped to entrench extreme jihadism in Pakistani society.

The Barack Obama administration has given off-the-record briefings that blame the ISI for Shahzad's abduction and killing – an allegation the ISI has rejected.

In his public remarks at a Pentagon briefing on Thursday, Mullen hwas less specific about the branch of government involvement, but left no doubt over who he thought was culpable. "It was sanctioned by the government," he said. "I have not seen anything to disabuse the report that the government knew about this."

He added that he thought Shahzad's killing was part of a pattern of eliminating troublesome journalists. "His [death] isn't the first. For whatever reason, it has been used as a method historically", adding that it raised worrying questions about Pakistan's future. "It's not a way to move ahead. It's a way to continue to, quite frankly, spiral in the wrong direction." The Pakistani government has set up a judicial commission to investigate Shahzad's death. It has requested copies of the journalist's email and mobile phone records and has summoned the assistance of 16 "prominent personalities" from the media and human rights organisations.