UN justice rapporteur Pablo de Greiff said Spain should scrap a 1977 amnesty law that stops victims from prosecuting the alleged perpetrators of such atrocities, which divide Spaniards to this day.
In a report, he urged Spain to scrap the amnesty and called on "the state institutions to show a decisive and determined commitment" to investigating and making sure that victims are compensated.
The amnesty was seen as a necessity by the leaders tasked with unifying Spain after Francisco Franco's death in 1975.
Groups representing victims' families say there are mass graves around the country containing the bodies of republicans killed by Franco's forces. His sympathisers say the republican side committed atrocities too.
In his report after 10 days of meetings with Spanish officials and civil groups, De Greiff bemoaned the "immense distance between the positions of most of the state institutions on the one hand and the victims and various associations" on the other.
He said the amnesty "has been used to shelve practically all of the cases brought before the judges" by people trying to prosecute alleged atrocities in the Spanish courts.
In Argentina, a federal judge is leading an investigation into forced disappearances and other alleged atrocities in Spain.
She has issued an international arrest warrant for two Spanish policemen accused of torture.
De Greiff on Monday expressed "concern" that Spanish state prosecutors had opposed that request in the case of one of the policemen.