The ISI and the police "deliberately failed" to properly probe Bhutto's killing which could have been averted, suggesting that the agencies could have been behind decisions like preventing an autopsy and hosing down the crime scene.
Questioning ISI's role in the immediate aftermath of Benazir Bhutto's killing, a UN panel has concluded that the presence of the all-pervasive spy agency "impeded an unfettered search for the truth".
The ISI and the police "deliberately failed" to properly probe 54-year-old Bhutto's killing which could have been averted, the panel said, suggesting that the agencies could have been behind decisions like preventing an autopsy and hosing down the crime scene.
The independent investigative panel was set up by the United Nations to investigate the facts and circumstances behind the death of Bhutto, at the behest of the Pakistan government.
The report noted that the presence of ISI is all pervasive in Pakistan, which creates an atmosphere of distrust that is highly disruptive in the country and the wider region.
"The investigation was severely hampered by intelligence agencies and other government officials, which impeded an unfettered search for the truth," the report said.
"Intelligence services, including the Inter-Service Intelligence Agency (ISI) were present during key points in the police investigation, including the gathering of evidence at the crime scene and the forensic examination of Ms Bhutto's vehicle, playing a role that the police were reluctant to reveal to the commission," it added.
Bhutto was killed on December 27, 2007 when a 15-year-old suicide bomber exploded himself close to her car in Rawalpindi where she was campaigning for the Pakistan Peoples Party (PPP) in parliamentary and provincial elections.
The inquiry of commission set up in 2009 to ascertain the facts and circumstances of Bhutto's death concluded that the death could have been prevented, and slammed the then Pervez Musharraf government for both failing to protect Bhutto and later failing to investigate her assassination.
"Most significantly the ISI conducted parallel investigations, gathering evidence and detaining suspects.
However, the bulk of the information was not shared with police investigators," the report said.
More broadly, the Commission concluded that the ISI had deep influence in politics and security of the nation, which should be performed by civilian institutions.
"No aspect of the Commission's inquiry was touched by credible assertions of the politicised and clandestine action by the intelligence services -- the ISI, Military Intelligence, and Intelligence Bureau," the report said.
"On virtually every issue the Commission addressed, the intelligence agencies played a pervasive role, including a central involvement in the political negotiations regarding Bhutto's return to Pakistan and the conduct of elections," it added.
The Commission also stressed that fear of the ISI prevented officials from doing their job of investigating Bhutto's death.
"These officials, in part fearing involvement by intelligence agencies were unsure of how vigorously they ought to pursue action that they knew, as professionals, they should have taken," the report said.
The Commission found, however, that threat warnings were communicated from the ISI directly to Bhutto but no positive action was taken to eliminate the threats.
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