In Friday's parliamentary debate on the draft, Pupovac said the government's Human Rights Office had not engaged experts while drafting the document, which he added was why the draft failed to clearly define the goals or ways of implementing the programme.
He said minority rights were one of the priorities in human rights protection, although a separate government office was in charge of their protection.
Pupovac said the draft national programme was overambitious because the government's Human Rights Office "claims it is authorised to coordinate ministries in the protection of human rights although that isn't its jurisdiction".
He said the part of the draft referring to the Second World War was unacceptable because it spoke, among other things, of "the homeland army which created the sovereign state".
"We recently saw Partisans and Chetniks being equated in Serbia, which elicited a fierce public condemnation, and now you are doing the same in this draft by equating the victorious antifascist coalition with those this coalition fought," said Pupovac.
He urged the government to withdraw the draft, saying it was necessary to draw up a new one.
Ivana Sucec-Trakostanec of the ruling Croatian Democratic Union (HDZ) said the draft was not incoherent but based on international directives and conventions.
Gordana Sobol of the strongest opposition party, the Social Democrats, criticised the draft, saying it did not define ways of implementation and that no money had been earmarked in the national budget for the implementation of the programme.
She reproached the government's Human Rights Office for giving little attention to the right to work and for either neglecting or failing to mention certain groups, like homosexuals.
Furio Radin, who represents ethnic minorities, said the actions of the security apparatus and the state administration's responsibility towards citizens should be included in the national programme as priority areas of human rights protection.
Slaven Letica of the Party of Rights said the freedom of the media defined in the draft should also include the protection of journalists from security services.
He said the recent case of five journalists claiming they had been under surveillance by the Counterintelligence Agency indicated that President Stjepan Mesic had been informed of that in detail. He also accused Mesic of being linked to media, mob and political circles.
Emil Tomljanovic of the HDZ said the draft national programme would regulate the protection and promotion of human rights in an integral way for the first time.