But Mr Obama said those who looted and started fires on Monday "should be treated like criminals".
The rioting came after the funeral of Freddie Gray, a black man fatally injured in police custody in Baltimore.
A week-long curfew has been announced and thousands of troops have been deployed to the city.
The National Guard has been sent to Baltimore to stop unrest for the first time since 1968, when some of the city's neighbourhoods went up in flames after the assassination of the Reverend Martin Luther King Jr.
On Tuesday evening, hundreds of protesters took to the streets to express their frustration with what they see as excessive police force.
The peaceful demonstrations were a contrast to the day before, when about 200 people were arrested as more than 100 cars were set alight and 15 buildings destroyed.
Mr Obama harshly criticised "a handful of people" for "senseless violence and destruction".
"That is not a protest, that is not a statement, they are stealing."
But the US president said the rioting had distracted from the frustration over Gray's death.
"This has been a slow-rolling crisis. This has been going on for a long time. This is not new. And we shouldn't pretend that it's new," Mr Obama said.
He added such problems would not be solved just by changes to policing.
"It would require everybody saying this is important, this is significant, and that we don't just pay attention to these communities when a CVS burns and we don't just pay attention when a young man gets shot or has his spine snapped."
At an afternoon briefing, Baltimore Captain Eric Kowalczyk was asked why the police had not responded with more resources to prevent fires and rioting.
He said police had originally deployed for a "high school event", expecting young students.
"I don't think there's anyone in the country that would expect us to deploy automatic weapons and armoured vehicles to an event with 13, 14 and 15 year olds," but saw it turned into an incident that drew in older troublemakers and escalated in violence.
It's been hours since the CVS was set alight here at Pennsylvania Avenue in Baltimore, but fire fighters are still battling the flames.
Earlier the stench of burning fumes filled the air as groups of people, armed with brooms and bin bags helped clear the mess from the night before.
As the day progressed the crowds of protestors built up. A line of police, wearing full riot gear and carrying batons and shields have been blocking one of the road's here.
For most of the afternoon protestors, danced and beat drums close by. There was the air of a carnival - a contrast to the violence this same area witnesses just the night before.
At one point things did get a little tense. A conversation between protestors and police ended with pepper spray being directed at the crowds.
But things have been calm overall. Protestors formed a human chain as the sun beat down on this bruised city. As nightfall a there'll be a curfew. The focus will be on what happens then.
Out of 235 arrests, 201 were adults, Capt Kowalczyk said.
He also noted there was a large group at a major intersection in Baltimore on Tuesday who were protesting peacefully. "That's what we're used to seeing in Baltimore."
Volunteers and city workers began cleaning up affected areas on Tuesday morning. Smoke still rose from buildings set alight the night before.
African-American Freddie Gray, 25, died on 19 April after suffering unexplained injuries to his spinal cord and spending a week in a coma.
Officials have suspended six police officers who were involved in the case.
Monday's clashes began hours after Gray's funeral.
Baltimore Mayor Stephanie Rawlings-Blake said it was very clear there was a difference between the "peaceful protests of those who seek justice" and the "thugs who want to incite violence".
A curfew was set to begin at 22:00 local time on Tuesday, continuing until 05:00 each morning for the rest of the week.
National Guard commander Linda Singh said that up to 5,000 troops could be put on the streets.
Freddie Gray's death is the latest in a string of high-profile cases where black men have died after contact with the police.
Nationwide protests followed the killing of unarmed black teenager Michael Brown by a white police officer in Ferguson, Missouri, last year.
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President Barack Obama has said police violence against African-Americans is a "slow-rolling crisis" after a night of violence in Baltimore.