SÃO PAULO, Brazil—Paulo Nascimento seemed to know what was coming when police caught him hiding in a home on a poor outskirt of São Paulo last November. The suspected car thief emerged pleading for his life with shrieks of "For the love of God!"

One officer slapped his face. Another kicked him in the rear. A third shot him.

Normally, Mr. Nascimento's death would garner little attention in a country where police kill more suspects than almost anywhere else in the world. Police in São Paulo state killed one suspect for every 229 they arrested last year, according to government figures, compared with one per 31,575 in the U.S. in 2011.

A clip from the Brazilian news broadcast "Fantastico" shows cell-phone footage of the arrest and final moments of Paulo Nascimento in São Paulo in November 2012.

But Mr. Nascimento's death stood out. An anonymous neighbor filmed his final moments, and a television news show aired the video the next day. Prosecutors have filed murder charges against four of Mr. Nascimento's arresting officers. The officers have pleaded not guilty; their trial is set to begin as soon as August.

In a country where many weary of violent crime justify police vigilantism, the video and pending trial are giving momentum to reformers who say the take-few-prisoners approach by Brazilian police is out of step with the aspirations of an emerging democracy seeking to lift a vast underclass into prosperity. They are reminders of Brazil's uneven development: Though the economy has surged, other areas such as criminal justice remain firmly in the Third World.

The problem is acknowledged by government officials, including São Paulo's governor, who has replaced his hard-line security chief with a mild-mannered lawyer vowing to take steps to reduce unjustified police shootings. In an interview, the new chief, Fernando Grella Vieira, said that the city has a "category of criminality" that will always lead to some justified police shootings. But, he added, "we aren't going to tolerate abuses on the part of the police."

Overview of a shantytown in São Paulo AFP/Getty Images

Two months after the Nascimento shooting, meanwhile, a separate incident drew attention to what prosecutors allege is one of the darkest sides of Brazilian police: Freelance death squads, called grupos de extermínio, in some precincts. As recently as 2010, four military police officers were sentenced to 18 years in prison for participating in one squad, which allegedly decapitated some of its victims.

Although neither the officers accused in the Nascimento killing nor anyone else has been charged with being part of a squad, investigators say other officers from the same precinct tried to sway the case by donning ski-masks and shooting up a bar not 50 yards from where Mr. Nascimento was shot. Seven people were killed and two wounded. Among those killed was Laércio Grimas, a lanky rapper known as DJ Lah. His hit song, "Click Clack Bang," warned young people, guilty or not, to run from police since "pardon is rare." Rumors had circulated that DJ Lah was involved with the video, locals told investigators. Prosecutors think he was targeted for it.

Under public pressure, São Paulo officials ordered ballistic tests done on every tactical weapon in the Nascimento officers' precinct. The test matched a bullet dug from a body to a police .40-caliber Taurus pistol. From there, officials found ski-masks and a shotgun with blood on the stock. Prosecutors charged nine officers with murder. The officers are disputing the charges.

Defense attorneys deny the DJ Lah and Nascimento murders are linked. And it later emerged that DJ Lah didn't make the video. Police documents show the person who did is now a protected witness.

Mr. Grella Vieira, who ordered the ballistics tests taken after DJ Lah was shot, said that since he took office and started a zero-tolerance policy toward abuse, investigators have arrested 40 officers who have been charged with murder or accessory to it, but who have pleaded not guilty. He called the arrests an important "pedagogical message" and pointed out that justifiable homicides by São Paulo police dropped by more than half to 66 in the first three months of the year from a year ago.

A video capturing the shooting of Paulo Nascimento by São Paulo police has drawn attention to alleged police brutality. TV Globo/Fantastico

As part of the crackdown, he has also prohibited police from transporting wounded suspects to hospitals, a measure sought by Human Rights Watch in a 2009 report. The nonprofit alleged that often such trips are coverups for executions of the wounded on the way to the hospital. Prosecutors allege such a fate befell Mr