"I want to know why he did this to the Libyan people," he told the BBC's Hardtalk programme. "I wish I were his prosecutor in his trial."
Mr Jibril added that he would welcome a full investigation into the colonel's death - as the UN has urged.
The statement comes as Libya's new leaders prepare to declare the country's liberation later on Sunday.
They have come under pressure to give a full account of Col Gaddafi's death in his hometown of Sirte on Thursday.
The US said this should be done in an "open and transparent manner". UN human rights Commissioner Navi Pillay called for a full investigation, as have major human rights groups.
Video footage showed Col Gaddafi being captured alive - and then dead. Officials say he was killed in crossfire.
A post-mortem carried out on the former leader's body on Sunday showed he had received a bullet wound to the head, medical sources said.
Acting Prime Minister Mahmoud Jibril told Hardtalk: "To be honest with you at the personal level I wish [Col Gaddafi] was alive."
He said he had wanted to ask the former leader why Libya had to endure 42 years of oppression under his rule.
Mr Jibril added that it would be "absolutely OK" to carry out a full investigation under international supervision into the killing, as long as Islamic burial rules were respected.
Correspondents say few Libyans are worried about the manner of their former dictator's humiliating end, which has been celebrated across the country.
Meanwhile the commander of the forces that captured Muammar Gaddafi has given details of the Libyan ex-leader's last moments.
Omran al-Oweib told the BBC that the colonel was dragged from a drainage pipe where he was hiding, took 10 steps and collapsed amid gunfire between NTC forces and Gaddafi supporters.
"I didn't see who killed, which weapon killed Gaddafi," Mr Oweib said. He added that some of his fighters had wanted to shoot the colonel, but that he had sought to keep him alive.
"I tried to save his life but I couldn't," he said.
Col Gaddafi's body - and that of his son Mutassim, who was also killed on Thursday - have been placed in a meat storage facility in the city of Misrata.
Conflicting reports The burial has been delayed, amid uncertainty about what to do with the body.
Officials from the National Transitional Council (NTC) have said they want a secret burial to prevent any grave being turned into a shrine.
National Transitional Council to issue a "declaration of liberation" Elections for a Public National Conference to be held within eight months The new body is to appoint a prime minister, an interim government and a constituent authority which will draft a new constitution within 60 days Constitution to be put to a referendum If the constitution is approved, general elections will be held within six months According to a military official in Misrata, a meeting in Benghazi on Sunday will discuss what to do with the corpse.
The formal declaration of liberation is due to take place on Sunday in the eastern city of Benghazi, the first city to break free from Col Gaddafi's rule. Elections should take place by next June, Mr Jibril has said.
"According to what we call the constitutional declaration, the first election after the liberation of the country... should be within a period of eight months maximum," Mahmoud Jibril told a conference in Jordan.
He said a new elected body would draft a constitution to be put to a referendum and form an interim government pending presidential elections.
Col Gaddafi, who came to power in a coup in 1969, was toppled in August. He was making his last stand in Sirte alongside two of his sons, Mutassim and Saif al-Islam, according to reports.
There are conflicting reports as to the whereabouts of Saif al-Islam, and Col Gaddafi's security chief - who are both at large.