Explaining his refusal of the declaration moved by eight nongovernmental organisations, Markovic said discussing an event which occurred outside state borders was not within the jurisdiction of the Serbian parliament.
He told Radio B92 he believed that all MPs were ready to adopt a document condemning crimes and asking that responsibility be established.
"I'm ashamed that some of the crimes were committed by Serbs. I'm also ashamed that some of them found refuge in my state, but we can't have someone scoring political or party points on victims who should rest in peace, and they will rest in peace when justice is done. All crimes must be legally condemned and legal and political possibilities must be provided, independently of political or party affiliation, for brining criminals to justice," said Markovic.
The Social Democratic Party described Markovic's refusal to put the draft declaration on parliament's agenda as cynical, hypocritical, irresponsible and politically harmful.
The Forum for Security and Democracy said in a statement on Friday that because of the refusal Markovic must no longer be parliament speaker.
On Saturday, Markovic announced the adoption of a document condemning crimes, but one to be moved and supported by MPs.
Serbia was shocked to see a video showing the killing of six Muslim youths from Srebrenica in 1995. The video was first showed at the Hague war crimes tribunal trial of ex-Yugoslav president Slobodan Milosevic. It was subsequently shown on TV stations in Serbia and served as identification material for the arrest of several perpetrators.
Serbian Deputy Prime Minister Miroljub Labos said on Saturday the crime carried out by the Scorpions unit had been perpetrated by a dictatorship.
"A couple of days ago we were all shocked to see someone tying children's hands behind their backs and killing them in cold blood only because they were of a different nationality. Those who committed that heinous crime must be prosecuted, and we as people must morally condemn that because it's something that mustn't be tolerated," Labus told reporters.
He added proceedings would be lawful and that those accountable would be brought to justice.