By Lily Kuo and Jennifer DobnerWASHINGTON/SALT LAKE CITY (Reuters) - The U.S. Justice Department sued two polygamist-dominated towns on the Utah-Arizona border on Thursday, citing religious discrimination and saying they operated for two decades as an arm of a breakaway Mormon sect.The complaint accuses the cities of carrying out the "will and dictates" of now-imprisoned sect leader Warren Jeffs, who is serving a prison term of life plus 20 years in Texas for raping two underage girls he wed in "spiritual marriages."Most of the residents of the twin towns of Colorado City, Arizona, and Hildale, Utah, are members of Jeffs' Fundamentalist Church of Jesus Christ of Latter Day Saints, which experts estimate has 10,000 followers in North America.The suit, filed in U.S. District Court in Arizona, said the police agency serving the two towns had sometimes deployed deputies to confront people about their disobedience to sect rules or to tell them to report to the sect leadership.Deputies also failed to arrest sect members who committed crimes against non-members, such as destroying their crops or trespassing, the suit added."City governments and their police departments may not favor one religious group over another and may not discriminate against individuals because of their religious affiliation," Thomas Perez, assistant attorney general for the Justice Department's Civil Rights Division, said in a statement announcing the suit.The suit said that at one point, when Jeffs issued an order for a sect member to return a runaway underage bride to her new husband in 2000, three deputies confronted the person to demand he return her to sect leaders, unaware he had already done so.At another point, when Jeffs banned dogs from households in 2001, deputies went house to house to round up the animals, then shot and killed them in a slaughter pit, the suit said.Additionally, the lawsuit accused the cities of refusing to issue building permits to non-sect members based on their religious affiliation, and that the utilities delayed water and electric service to non-members.CITIES DENY ALLEGATIONSSalt Lake City-based attorney Peter Stirba, who represents Hildale, and Phoenix-based attorney Jeff Matura, who represents Colorado City, both said the cities denied the allegations.Matura called the move a "heavy-handed" attempt by federal officials to accomplish what Utah and Arizona officials had been unable to do for decades: dismantle the FLDS communities for their religious practice of polygamy.The polygamist sect, which Jeffs continues to lead despite his 2011 child sexual assault conviction, has been condemned by the mainstream Mormon Church, which long ago disavowed polygamy.Raids on the twin communities dating back to the 1930s by state and federal authorities in both states had been unsuccessful, and most of the legal actions brought against city officials in the past had also failed, Matura said.The lawyers said none of the allegations was new - some date back to 2000 - and many had been the subject of earlier lawsuits or investigations that had already been resolved."It's a rehash," Stirba told Reuters. "But for whatever reason now the federal government thinks it's appropriate to do something about it."In 2008, for example, a federal judge in Utah tossed out a lawsuit from a former church member alleging religion-based discrimination by police, Stirba said. A 2007 probe by police academies in both states ended with four of the department's six officers cleared of allegations of wrongdoing. Two resigned.Arizona Attorney General Tom Horne welcomed the lawsuit, saying he had proposed legislation last year that would have barred the sect from controlling law enforcement in Colorado City, but that the bill had not passed. Utah's legislature also failed to pass a similar proposal last year.Two weeks ago, Horne announced his office would provide $420,000 to the Mohave County Sheriff office for overtime pay so officers could patrol Colorado City 16 hours a day.(Reporting By Lily Kuo; Writing by Cynthia Johnston; Editing by Peter Cooney)