"I believe the federal government has grown out of control, threatening the rights, liberties, and property of the people," goalie Tim Thomas said in a statement.
The decision to stay away, Thomas said, "was not about politics or party, as in my opinion both parties are responsible for the situation we are in as a country."
Bruins general manager Peter Chiarelli told reporters that Thomas, who will be an all-star later this month, won't be suspended for his absence.
Meanwhile, team president Cam Neely told Joe Haggerty of Comcast Sportsnet New England he would have like to see the only American member of the Bruins' championship team attend the event.
"Everybody has their own opinions and political beliefs. He chose not to join us," Neely said. "We certainly would have liked to have him come and join us. But it's his choice. It's obviously not a choice most of the guys ... well all of the guys came except for Tim. But it's his decision and his choice."
Even though Thomas, the playoff MVP and the Vezina Trophy winner as the league's top goaltender in the regular season, skipped the event, many of the Bruins made it to the White House.
The Bruins won their first Stanley Cup title in 39 years last June after a bruising seven-game final against the Vancouver Canucks.
It was the latest in a string of Boston sports championships, including the Celtics in 2008, the Red Sox in 2007 and the New England Patriots in 2005. The Patriots play in next month's Super Bowl.
"The Bruins, the Sox, the Celtics, now the Patriots. Enough already, Boston," Obama said during a ceremony in the East Room of the White House. "What's going on, huh?"
Obama also jokingly invoked some New England slang in welcoming the Bruins, along with the Stanley Cup, to the White House.
"I know you are all wicked happy to be here," he said.
The president said there was no better image of the Bruins' dominance than when Zdeno Chara, the team's six-foot-nine defenceman, hoisted the Stanley Cup above his head in Vancouver in celebration last spring.
"Which is, I'm sure, the highest that the Stanley Cup had ever been," he said.
Obama drew laughter from the crowd when he cited the scrappy play of Bruins forward Brad Marchand, who emerged as a star with five goals in the last five games of the finals against Vancouver.
"'The 'Little Ball of Hate' shrugged off the rookie jitters," said Obama, adding "What's up with that nickname, man?"
Obama praised the teamwork of the six-time champions.
"Together, these players proved that teamwork is everything," he said. "It can overcome injuries, it can overcome long odds."
Obama praised the team for its work off the ice as well, noting the Boston Bruins Foundation has donated more than US$7 million to charities in New England.