Clinton cancelled a speaking engagement in Virginia after news of the incident emerged.
A witness said that one of the hostages who was released by the man told her that he had explosives strapped to his body.
"A young woman with a 6-month or 8-month-old infant came rushing into the store just in tears, and she said, 'You need to call 911. A man has just walked into the Clinton office, opened his coat and showed us a bomb strapped to his chest with duct tape'," Lettie Tzizik told WMUR TV during the incident.
Police teams, including bomb disposal crews, were dispatched to the scene.
The incident came weeks before the first presidential candidate nominating contests in Iowa, and the first primaries in New Hampshire on January 8.
The campaign offices of rival Democratic presidential candidate Barack Obama in Rochester have also been evacuated, as well as several businesses.
Clinton and Obama are the Democratic front-runners in the race for the US presidency in 2008.
Anthony Ejarque, 42, owner of Slims Texmex Saloon in the street where the campaign office is located, said police evacuated 30 to 40 customers and workers from his restaurant during the incident.
"They came right in and asked everyone to get up and leave and evacuate the kitchen and everybody," Ejarque said.
Ejarque said during the stand off that the street was quiet but that "there apparently is a guy with a bomb in the Hillary building, which is right across the street for us".
Rochester is the site of one of 16 of Clinton's offices in the state, according to Clinton's campaign website.