The report covers the period from 2014 to 2018 when the then leftist Farabundo Marti National Liberation Front (FMLN) government waged a campaign against criminal gangs blamed for one of the highest murder rates in the world.
Investigators examined 48 cases in which 116 people were "brutally assassinated" by the police, said Raquel Caballero, head of the Prosecutor's Office for the Defense of Human Rights.
"We have identified patterns of behavior of members of the national civil police," she told a news conference in the capital San Salvador.
A spokesman for the ministry of security and justice declined to comment.
El Salvador is one of a trio of countries in Central America, along with Guatemala and Honduras, that has seen thousands of desperate migrants flee raging gangland violence and bleak economic prospects over the past couple years.
Salvadoran authorities blame the gangs for the violence, even as rights groups have accused the police of carrying out extrajudicial killings and other rights violations in confrontations with gang members.
Caballero's office launched its investigation in August 2018 in response to a rise in reports of police abuse and completed its work in May.
One of the more disturbing findings was the level of police impunity, she said. In the 48 cases of excessive police force, only 19 were prosecuted and two cases led to convictions.
She urged the new government to act on the report's findings.
"It is important that ... the facts are investigated, that responsibilities are deduced, that the respective convictions are prosecuted and obtained," Caballero said.
President Nayib Bukele, who took office in June, has ruled out negotiations with criminal gangs and vowed to go after their finances in a bid to bring down a sky-murder rate.In 2018, the country recorded 50.3 homicides per 100,000 inhabitants, one of the highest levels in the world, according to the United Nations.