The rights watchdog said it documented "excessive use of force against peaceful demonstrators" by officers from Spain's national police and Guardia Civil forces in the city of Girona and two hillside villages, Aiguaviva and Fonollosa.
It said police charged protesters without warning and used batons and shields to hit them on their heads, arms, legs and torsos in Girona, while in Aiguaviva and Fonollosa police used batons and threw people to the ground.
"The police may well have had the law on their side to enforce a court order but it didn't give them the right to use violence against peaceful protesters," said Karthik Raj, western europe researcher at HRW.
Images of alleged police violence were beamed around the world after the October 1 referendum, which Catalan's separatist authorities claim saw 90 percent of those who voted support a split from Spain.
At least 92 people were injured and hundreds required medical assistance.
It took the central government five days to apologise to those hurt, with two officials saying they "regretted" the violence.
HRW said that as of last week, 23 different courts in Catalonia were examining allegations of police misconduct, with one investigating complaints made by 36 individuals relating to 17 sites in Barcelona.
Other rights groups contacted by AFP criticised the Spanish police's conduct during the referendum.
"We saw excessive use of batons including people hit in the face, which is forbidden by the United Nations," said Ignacio Jovtis, an observer for Amnesty International in Spain.
He also said police had fired rubber bullets that are banned under international rights conventions.
Jose Cobo, a spokesman for the Spanish Association of Civil Guards, however said that police "did not use excessive force, and responded gradually and proportionately to the illegal vote".
He said the number of reported injuries had been "totally exaggerated" insisting that only two people required hospital treatment on October 1: one hit by a rubber bullet and another who suffered a heart attack.
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