"Prosecutors are acting in a way that tends towards disqualifying complaints, obstructing procedures and even showing a lack of interest in the process, hindering the clarification of facts by judicial authorities," the organisation said in a statement.
It accused prosecutors of "not fulfilling their role of driving investigations."
It cited as an example attempts by prosecutors to use alleged violence by voters against security forces as a reason to "dismiss judicial investigations" into reported police violence.
Amnesty also called on the Spanish government to prohibit the use of rubber bullets after one man in Barcelona lost an eye after being hit by one on the day of the referendum on October 1st.
"Rubber bullets that are being used in Spain should be banned for being highly imprecise," said Esteban Beltran, head of Amnesty Spain.
He added that they were used in Spain to disperse crowds, while international norms dictate they should not be used for that reason.
Neither the prosecutors' office in Madrid nor the interior ministry immediately responded to requests for comments.
Images of alleged police violence were beamed around the world after the referendum, which Catalan 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.
But several hundred complaints for police violence were filed before eight Catalan courts. Amnesty lists 457 of them before just two tribunals.
The interior ministry, meanwhile, said close to 100 agents were also hurt.
Human Rights Watch has also accused police of using "excessive force."
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 the villages of Aiguaviva and Fonollosa police used batons and threw people to the ground.