Gray is one of a number of black men who have died under questionable circumstances during police encounters in recent months. Last year, weeks of protests followed the fatal shooting of unarmed black teenager Michael Brown by a white officer in Ferguson, Missouri, and the chokehold death of Eric Garner in New York City.
About 2,000 people marched on Saturday afternoon through downtown Baltimore, pausing at the Camden Yards ballpark, the home of the Orioles professional baseball team, where some demonstrators shouted chants at officers standing guard.
Citywide, police arrested 34 people who ignored orders to disperse, Batts said, and at least six officers were hurt in skirmishes. Several police vehicles were damaged.
"A small contingent of yesterday's protesters caused violent disruptions downtown and in west Baltimore last night and early this morning after what had been mostly peaceful protests," police said in a statement.
The department beefed up its presence downtown and across Baltimore on Sunday. Extra officers will be deployed in the area through the night and into the week.
Six Baltimore police officers have been suspended in the Gray case, and an internal police investigation is under way.
Protesters have called for the prosecution of the six officers involved in Gray's arrest and for reforming police tactics. Police have yet to explain when and how Gray was injured.
Standing in the street outside the wake on Sunday, a small group of people held signs reading, "Honk for Freddie." Passing cars frequently sounded their horns.
Among those attended the viewing was Dwayne Peay, who called for calm out of respect for the wishes of Gray's family.
"We want no violence, just peace for everyone, including the Baltimore police department," Peay said after exiting the funeral home.
Funeral services for Gray are scheduled for Monday morning, followed by his burial.
Several events were postponed or canceled on Sunday due to safety concerns after Saturday's protests, including the SPCA's annual March for the Animals fundraiser, the group said on its website.
Sunday afternoon's game between the Orioles and the Red Sox at Camden Yards went ahead on schedule.