Police spokesman Jamie Kenneally said the arrests began about 1:30 a.m. Tuesday and were mostly for trespassing.
The protesters, part of the national Occupy Wall Street movement, had tried to expand from their original site in Dewey Square to a second site across the street, along the Rose Kennedy Greenway. A local conservancy group recently planted $150,000 worth of shrubs along the greenway and officials said they were concerned about damage.
Boston police had warned protesters for several hours that they would have to return to Dewey Square, where a tent city has been steadily growing, and issued leaflets saying protesters could not occupy the greenway.
Early Tuesday, about 10 police officers patrolled the greenway, some with dogs. Protesters who went to a nearby police station to bail people out did not find anyone there, and by 4 a.m. they had returned to their encampment to discuss how to raise $4,000 in bail money.
Boston resident Matt Hollander, 25, said a group of veterans carrying American flags were standing in between police and the protesters when officers advanced on them. One veteran, he said, was pushed to the ground and a group of protesters fell in a heap.
"If they wanted to arrest us they could have done that without pushing us...without tramping the flag," Hollander said.
Another protester, Shawdeen Vatan, 21, of Arlington, Mass., said she was not surprised at what happened.
"We're being seen as a legitimate organization," she said. "People are panicking and trying to get us out of here."
Police did not report any arrests from an earlier standoff, where hundreds of students from 10 area colleges marched through downtown Monday, briefly confronting police while attempting to hang a banner on a Boston bridge.
The protesters gathered on Boston Common and marched in front of the Massachusetts Statehouse carrying signs that read "Apathy isn't working, Raise your voice," and chanting slogans like "Fund education, not corporations" and "We got sold out. Rich got bailed out."
They later marched to a Charlestown bridge near the city's North End neighborhood hoping to hang a banner.
Police blocked the bridge, which was closed for about an hour before the protesters dispersed. Two demonstrators appeared to scuffle with officers during the standoff. Police did not immediately report any arrests.
The protesters on Wall Street and in Boston and other cities have described themselves at the "99 percent" - referring to what they say are the vast number of Americans struggling to pay their bills while the income gap between the rich and middle class widens.
In Seattle, participants in a protest in downtown Westlake Park said late Monday that they were told the park is closed and they may be arrested if they remain.
Sharla Laurin, an Occupy Seattle peace and safety facilitator, said announcement was made over a loudspeaker. Protesters heard from the mayor's office that there weren't supposed to be any arrests but from Seattle police on the scene that there might be.
Police spokesman Detective Mark Jamieson said he had no information about any arrests.