Bolsonaro, who takes office on January 1, made the controversial remarks late Tuesday in a live video feed on his Facebook page.
The extreme right-wing politician was elected in October on a hardline anti-crime and anti-corruption platform and has been dubbed the “Tropical Trump.”
“Everybody knows what is happening in France. Some parts of France are simply unlivable,” Bolsonaro said on Facebook.
He said that, despite a good welcome by the French, migrants were not integrating.
“You know how those people are, right? They have something in them, they don't give up their roots and they want to make their culture, their acquired rights and their privileges prevail,” he said.
“France is suffering because of that. Part of the population, part of the military, some of the institutions are starting to complain about that. We don't want that for Brazil.”
It was not clear what recent events prompted Bolsonaro's outburst. Nor did he explicitly say whether he was referring to Muslim migrants, though those with North African heritage form the biggest group of migrants in France after Europeans.
France is currently in the grip of “yellow vest” anti-government protests unrelated to migration.
It has been rocked by a number of recent deadly attacks, notably in November 2015 in which 130 people were murdered in Paris by radicalized French- and Belgian-born gunmen, and last week in the city of Strasbourg where a French-born ex-convict killed five people in a rampage claimed by the Islamic State group.
Aligning with Trump
The comments by Bolsonaro recalled those made by Donald Trump in December 2015 as he was campaigning to become US president.
Speaking to US network MSNBC, Trump claimed “they have sections in Paris that are radicalized, where the police refuse to go there. They're petrified. The police refuse to go in there.”
Trump also said parts of London were similarly dangerous, and used those assertions to justify a “total and complete shutdown of Muslims entering the United States.”
After becoming president, Trump issued an order that largely bars citizens from five Muslim-majority countries getting US visas.
Bolsonaro did not say whether he would impose tighter immigration controls, but did repeat that he will pull Brazil out of a nonbinding global migration pact ratified by the UN General Assembly on Wednesday.
“Unfortunately, Brazil… signed the pact. We are not against migrants, but we must be have very rigorous criteria for those entering Brazil. We are going to denounce and revoke this pact on migration,” he said.
In the same Facebook video, Bolsonaro said he would do everything possible to counter the governments of Venezuela and Cuba, calling their leaders “dictators” and saying neither were being invited to his inauguration.