He was speaking at an HHO award ceremony and on the occasion of International Human Rights Day, which is observed on December 10.
Puhovski said that instead of modernising police work, the use of weapons was being advocated, and added that the HHO would fight for everyone's human rights.
In a report, the HHO pointed to poor results in investigating and finding perpetrators of assaults on members of the Serb minority because only one of 34 incidents had been solved.
Puhovski added the media coverage of minorities had deteriorated for the first time since 1996.
He said it was unacceptable that a dozen persons accused of war crimes had been released pending trial, while at the same time pressure was being exerted on witnesses of crimes.
Puhovski went on to say that social rights had seriously deteriorated and that the protection of the elderly and children was increasingly deteriorating.
According to the HHO report, the situation in the judiciary was also poor. Puhovski said there was a series of final sentences containing untenable verdicts and explanations.
Puhovski went on to say this human rights situation pointed to the responsibility of the authorities, society and all who had not reacted, but also to the responsibility of international factors because they decided to open Croatia's European Union accession negotiations in the year when the human rights situation had deteriorated.
He added that the state of bodies of security, which should be a key factor in the protection of human rights, was worse than before.
President Stjepan Mesic, who attended the award ceremony, said it was lamentable that the state of human rights was deteriorating and that for it to improve, state mechanisms should control institutions.
"The (HHO) report is based on facts and there is no reason to doubt it," he said.