The vast majority of protesters have been peaceful, but a "small minority" were putting people at risk and harming the very communities the protests are intended to help, Obama wrote in an online essay posted on Medium.
Obama, a Democrat who served two terms as president prior to Republican Donald Trump's administration, said the violence was "compounding the destruction of neighborhoods that are often already short on services and investment and detracting from the larger cause."
The United States has been rocked by six straight nights of tumult over the death last week of a black man in Minneapolis, George Floyd, after a white police officer pinned him to the ground by kneeling on his neck.
Obama's latest remarks came three days after his first comments on the Floyd case, which called for justice but did not mention the violent nature of some protests. His shift in tone on Monday came as some protesters have set fires, smashed windows and looted stores, forcing mayors in large cities to impose nighttime curfews.
On Sunday, presumptive Democratic presidential nominee Joe Biden, who served as Obama's vice president and will face Trump in the Nov. 3 election, also called for an end to the violence.
"Protesting such brutality is right and necessary," Biden said in a statement. "But burning down communities and needless destruction is not."
Obama, who remains perhaps the most popular figure in the Democratic Party, endorsed Biden for president in April and has said he will campaign for him in the months ahead.
Largely avoiding politics since he left office in 2017, Obama recently has been critical of Trump's handling of the coronavirus pandemic.
As the first black U.S. president, Obama dealt with civil unrest in cities such as Ferguson, Missouri, and Baltimore, where there were widespread, sometimes violent, protests over the deaths of young black men at the hands of the police.
In both cases, Obama was critical of the violence, saying they hindered efforts to curb police misconduct. In 2015, during the Baltimore protests, he blasted "the criminals and thugs who tore up the place."
Obama's Justice Department launched probes into police departments in those cities and others such as Chicago in an effort to bring about internal reforms, a practice the Trump administration has employed much less frequently.
In his Medium essay, Obama urged protesters not to be cynical about politics, arguing that electing new leaders on the national and local levels would bring about change.
"Eventually, aspirations have to be translated into specific laws and institutional practices — and in a democracy, that only happens when we elect government officials who are responsive to our demands," he said.