Speaking on Croatian Radio, Milanovic said he would propose with constitutional amendments to lift the statute of limitations on all murders, which would include political assassinations, and the commission of inquiry would be chaired by opposition leader Tomislav Karamarko.
The commission would also investigate Josip Perkovic, a former Yugoslav and Croatian secret agent wanted by Germany for his role in the 1983 Djurekovic murder.
Croatia in June amended the law on judicial cooperation in criminal matters with European Union countries to limit the application of the European Arrest Warrant (EAW) to crimes committed after August 2002. The law was publicly dubbed Lex Perkovic and the European Commission criticised Croatia over the amendments.
Speaking of the dispute with the Commission, Milanovic said the government wanted Croatia to be treated equally as other EU members, some of which are exempt from EAW application, stressing it was clear from the start that this was not about "protecting one man."
He said these were "difficult topics" which should be discussed sensibly, while Karamarko's Croatian Democratic Union (HDZ) "is trying to make a racket and is misinterpreting everything."
Milanovic said the purpose of the constitutional amendments would be to see "who is hiding what in this country, who hid certain evidence for 20 years, who was at the helm of intelligence services, who had political influence."
He voiced surprise that the HDZ had not proposed the founding of a parliamentary commission of inquiry, given its senior officials' claims "that there existed a system of protection of communist assassins."
As for Perkovic, Milanovic said he would have to appear before a judicial body - the Croatian state prosecutor if the statute of limitations was lifted, or be extradited to Germany. He said those "claiming that this is something which should be tried by Germany... would like it most if it was not talked about in Croatia. We want this to be talked about in Croatia."
If all that is being said is true, the Djurekovic assassination was a crime planned and committed by Croats, the victim was a Croat, the place of execution was Germany, yet it could have been Austria or another state, said the PM.
"The place for the trial and shedding light on this case is Croatia, and when someone from the top of the HDZ tells me that a fair trial can't be ensured in Croatia, so the person should be turned over to Germany, I think the person who says that should give up Croatian citizenship. That's shameful."
He said that when the statue of limitations was lifted, the state prosecutor would be able to do everything it failed to do in the past and "decide whether to launch an investigation."
"Because if we don't change the constitution... and lift the statue of limitations, there is no extradition or trial in Croatia," he said, adding that this should be discussed sensibly.
The PM went on to say that the HDZ was interpreting wrongly the constitutional law on national minorities' rights too. Some people in Croatia, he said, "evidently have no shame or responsibility."
He reiterated that the only reason for limiting the application of the EAW was the danger of Croatian citizens being tried for war crimes under the principle of universal jurisdiction at any court in Europe. "It's something completely beyond our control... And it is my duty as statesman and of my collaborators to warn about this... If this gets through to enough ears and heads in Croatia, I did my job."
Milanovic said this was a transitional period and that Croatia was in consultations with the European Commission.
"We must learn that we are an EU member, that we have rights, that states there should be treated equally and that the EU was founded on the principle of equality of states before EU contracts and acts," he said, adding that the EAW was completely unaligned with that fundamental principle.
"Croatia is simply asking that everyone be equal, that's all," he said, adding that "Croatia will behave as such."