In continuing verbal sparring over the circumstances of the murder of Shahzad, Mullen hinted that Pakistan government may have sanctioned the abduction and subsequent killing of Shahzad.
"The reports that he was killed and there were government officials who had sanctioned that... I have not seen anything to disabuse the report that the government knew about this. But I can't, would not be able to walk in that here is the string of the evidence that I have to confirm it," Mullen told reporters at a Pentagon Press Association luncheon in Washington.
His remarks triggered fury in Islamabad adding to even more strain in Pak-US relations which have teetered since the American raid that killed Osama bin Laden in Abbottabad.
Reacting to Mullen's comments, a Pakistan government spokesman said: "If it is true, then the statement is extremely irresponsible." The remarks "will not help in investigating the issue" of Shahzad, the unnamed spokesman told state-run APP news agency.
The spokesman said: "some elements are trying to use" the killing of Shahzad against the elected democratic government and Pakistan.
"We cannot say anything except expressing regret on it."
Though Mullen acknowledged he could not directly link the killing to the ISI, he was the first US official to make such a public allegation.
The Pakistan government spokesman said an "independent, non-partisan and autonomous commission" has already established to probe the killing of Shahzad.
The commission has requested people to provide any relevant information they have regarding the killing.
"If anyone has to share anything at the national or international level, it should be shared with the commission... If any statement is issued other than this way, it will be considered an attempt to influence the proceedings of the commission," the spokesman said.
Shahzad was abducted while driving from his house to a TV station in Islamabad on May 29, two days after he alleged in an article that Al Qaeda had infiltrated the Pakistan Navy.
His body, bearing marks of torture, was found the next day in a canal in Punjab province.
Journalists' associations and rights groups alleged intelligence agencies were responsible for the killing, a charge denied by the Inter-Services Intelligence. Shahzad had also told colleagues about receiving veiled threats from the ISI.