"While unions have the right to legally advocate on behalf of their members, my office will not tolerate the conduct of those who use violence to further union goals," U.S. Attorney Zane David Memeger said at a news conference announcing the arrests.
Dougherty's lawyer, Joel Trigiani, declined to comment on the specific charges facing his client but described him as a tireless advocate for his members.
"This is a guy who has committed his life to union work," Trigiani said.
While FBI agents were combing through records at Local 401's headquarters in Northeast Philadelphia on Tuesday, union officials were keeping quiet. The ironworkers' international condemned using violence as a tactic.
"We have never and will never tolerate any of the alleged acts contained in the accusations," union president Walter W. Wise said in a statement.
According to the 49-page indictment, Dougherty, 72, coordinated the campaign of sabotage and extortion, urging members to picket, threaten, and destroy the property of contractors who ignored threats against hiring nonunion employees.
At the meetinghouse work site, prosecutors said, three union members cut steel beams and set fire to a crane in December 2012, setting the project back weeks and costing the contracting firm, E. Allen Reeves Inc. of Abington, more than $500,000.
At the time, Local 401 business agent Edward Sweeney told reporters that he knew nothing about the fire, saying only that he had asked the company to hire union workers.
Authorities said Tuesday that Sweeney ordered the attack.
"It's about time. This has been going on for all of my career," firm president Robert N. Reeves Jr. said Tuesday.
Dougherty vowed that his members were not involved when the union came under scrutiny in the June 2010 melee outside the Toys R Us work site on Gulph Road near the King of Prussia mall.
The rumble began when nonunion workers from Lebanon, Pa.-based Maura Buildings arriving at the site encountered a wall of pickets, according to a police report. Maura employees called police, whereupon three of the pickets smashed the workers' trucks with baseball bats and hit one of the nonunion employees in the face.
"We have picket lines all the time," Dougherty told The Inquirer at the time. "We know what you have to do. You can't have any violence on the picket line."
It wasn't just nonunion laborers that drew Local 401's ire, prosecutors said.
A near-street brawl erupted last July when union members felt that the carpenters' union had poached work from them at a site at 19th and Arch Streets.
"I hate to say it," Sweeney told one ironworker in an exchange quoted in Tuesday's indictment, "but you hope to get cancer, so you can go there and just shoot every [member of the other union] down there."
Violence was not just a tactic in the ironworkers' toolbox, prosecutors said. It is deeply ingrained in the structure of their organization.
Members earned spots on the union's board based on their involvement in work-site attacks, and leaders relished their reputations as strong-arm enforcers, according to the indictment.
Local FBI special agent in charge Edward J. Hanko joked that the leaders' brazenness reminded him more of his past investigating mob cases in New Jersey.
Prosecutors also claimed that Dougherty (no relation to electrical workers union boss and Democratic heavyweight John "Johnny Doc" Dougherty) relied on the union's considerable ties to state and local officials to further his aims.
Asked to elaborate Tuesday on a potential political component to his investigation, Memeger remained tight-lipped and stressed that the probe was continuing.
"You're constantly weighing what evidence you can bring before a grand jury and get an indictment," he said. "We felt it important to bring the charges now."
At least two candidates sought to distance themselves from the indicted officials.
U.S. Rep. Allyson Y. Schwartz, a Democratic candidate for governor, announced that her campaign had donated to charity the $10,000 contribution she received from the local.
State Auditor General Eugene DePasquale quickly followed suit, giving up $7,500 he took from the group in 2012.
One candidate, though - State Rep. Brendan Boyle, a Democrat running for Congress in Pennsylvania's 13th District - defended the ironworkers' contribution of $10,000 to his campaign last year.
"Certainly we don't condone any of the alleged actions of a few individuals," Boyle said in a statement. "But this alleged incident shouldn't be used as an excuse to attack the important work unions do to reduce the growing gap between the rich and everyone else."
Contributing to this article were Inquirer staff writers Allison Steele, Thomas Fitzgerald, and Amy Worden.