No suspects have been announced by police, but Franco, who was 38, had ruffled many feathers - and that was her mission.
Police say her vehicle may have been tailed several miles before the killer fired, killing Franco and her driver, leaving an aide wounded, then disappearing.
Franco's death comes just weeks after she was appointed rapporteur for a special commission that the city council created to monitor the government's use of the military to take control of all public security through the end of the year in Rio. A press officer in the back seat was injured, but survived, the officials said.
Ms. Franco grew up in Maré, a district in northern Rio de Janeiro that is among the largest in the city's constellation of favelas, largely impoverished districts that were initially settled by squatters. Many of those who took to the streets say that they hope that these two deaths will promote a national movement, just as U.S. students in Parkland, Florida formed a movement to protest against lenient gun laws after the shooting at one of the district's high school last month.
As a black woman who got the fifth highest vote count in Rio's 2016 council elections, Franco stood out in the region's male- and white-dominated politics. "Another homicide of a young man that could be credited to the police".
The killing came just weeks after the Brazilian government chose to let the military take over all security operations in Rio to control the city's increasing crime rates.
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Security consultant Paulo Storani, a former commander of Rio's elite police force known as the BOPE, warned against jumping to conclusions about the police or blaming the military intervention, which he believes will ultimately be ineffective.
Franco, 38, was an outspoken critic of police violence and the deployment of the army into poor neighborhoods.
Franco, who was raised in the Mare complex of slums, long one of Rio's more unsafe areas, received over 46,500 votes in the 2016 election.
A "full investigation" is going to be carried out over the death, confirmed the head of public security Richard Nunes. Mathews Melo was leaving church. "This has always happened and with the (military) intervention things have gotten worse", she wrote on her Twitter. "This week two youth were killed and tossed into a ditch".
Police said they were investigating whether this was a targeted assassination.
Christian Aid has condemned this week's killings of human rights defenders in Brazil and called for urgent inquiries into their deaths. Finance Minister Henrique Meirelles, who is contemplating a bid for the presidency, said the assassination underscores the need of the Rio military operation.
"In the women's fight, we are shattered", Lucia Cabral, who has worked with Franco on human rights issues, told Newsweek from a protest in Rio's city center.