Other accusations include police helping euthanize the town's dogs at Jeffs' order, keeping a woman in jail overnight on an inaccurate underage alcohol charge and threatening arrest of non-FLDS children if they continued to play at a city park.
The lawsuit also accuses town water and power utilities of refusing to provide housing permits and utility hookups to nonmembers or to allow them to move into homes.
"Religious freedom is a cherished principle of our democracy," said Thomas Perez, assistant attorney general for the Justice Department's Civil Rights Division, in a news release. "No individual in the United States should be targeted for discriminatory treatment by a city, its officials or the police because of his or her religion."
No specific victims are named in the lawsuit. It seeks unspecified damages and injunctions against town officials.
Attorneys for Hildale and the utilities decried the lack of evidence in the suit, pointing to other lawsuits and investigations into town marshals that have failed to turn up wrongdoing.
"We think it's an unfortunate ... exercise of federal power," said defense attorney Peter Stirba. "Not one adjudication at any court or administrative body has found that town officials have discriminated against anyone."
Hildale City Attorney Blake Hamilton said federal attorneys approached him in December seeking to, "in essence, take over the community" and rebuild the police and government.
"We just have to show them what the real facts are," said Colorado City attorney Jeff Matura. "They're getting a very one-sided version of what Colorado City is really about."
Utah Attorney General Mark Shurtleff applauded Thursday's filing, saying he had long sought federal involvement.
"We have offered our full cooperation and collaboration with the Department of Justice to aggressively investigate and address these complaints," he said in a news release.
Arizona Attorney General Tom Horne said he was "very pleased that the U.S. DOJ has taken legal action to join us in this fight" and looks forward to "justice being served."
Allegations of civil rights abuses have long swirled around Hildale and Colorado City and in 2010, then-Arizona Attorney General Terry Goddard filed a civil rights complaint in the case of Ronald Cooke, a disabled man who said he and his wife were forced to haul water because the town refused to connect them with running water.
A federal judge is now weighing a motion for summary judgment in that case.
Six town marshals have been decertified by Arizona since 2003, most for expressing their support and loyalty for Jeffs. This year lawmakers in Arizona and Utah introduced bills to disband the town's joint police department, but both failed.
The Arizona Attorney General's Office announced earlier this month it would give the Mohave County Sheriffs' Office a $420,000 federal grant for more overtime patrols of the city.
Jeffs, 56, is serving a life sentence in a Texas prison for sexually assaulting two girls, ages 12 and 15, who he took as polygamous wives. He is nevertheless considered the leader of the FLDS.
The Polygamy Blog: www.sltrib.com/blog/polygblog