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A federal agency has assessed fines of almost $2 million against the Fundamentalist Church of Jesus Christ of Latter-Day Saints, a business and leaders of both for using children and unpaid laborers at a 2012 pecan harvest in southern Utah.

The harvest has been at the center of lawsuit in federal court in Salt Lake City that has touched on religion as much as labor law. Besides the church and the business — called Paragon Contractors Corp. — the U.S. Department of Labor has fined Lyle Jeffs, the man who runs the day-to-day operations of the FLDS. He is the brother of its imprisoned leader, Warren Jeffs.

Two Paragon officers, Brian Jessop and Dale Barlow, were also fined.

In all, the Labor Department assessed fines of $1,964,450. The amount is to be paid jointly, according to an email from Labor Department spokesman Juan Rodriguez.

The fines were issued April 20, with a 15-day deadline to contest them. Rodriguez's email said Paragon, Jessop and Barlow are appealing.

Rodriguez's email also said the Labor Department has concluded the "subpoena enforcement litigation" that was the basis of the lawsuit in federal court. The Labor Department had been trying to force Paragon, the FLDS Church, Lyle Jeffs and another brother, Nephi Jeffs, to answer its subpoenas and questions.

The case gained national attention last year when federal Judge David Sam cited the U.S. Supreme Court decision in a case involving the retailer Hobby Lobby to rule that one man suspected of having ties to the FLDS, which endorses polygamy, did not have to answer questions about the workings of the church.

Lyle and Nephi Jeffs also used the ruling to try to avoid answering questions under oath about their role in the harvest. Sam sided with the brothers on some questions, but said they had to answer others.

Attorneys for Paragon, Jessop, Barlow and Lyle and Nephi Jeffs did not respond to messages seeking comment on Tuesday. Rodriguez's email said Labor Department employees involved in the case were not available Tuesday.

Rebecca Musser, who was once married to Lyle Jeff's father, Rulon Jeffs, and later testified against FLDS men on trial for sexual assault of children in Texas, welcomed the fine. But she said criminal prosecutions are what is needed to stop the use of children as laborers. She also worried the fine will — one way or another — be paid by the people following the Jeffs family rather than the offenders.

Pecan picking is "one of the more innocent ways they have broken the law," Musser said of FLDS leaders.

The probe began after a December 2012 broadcast by CNN. It showed hundreds of women and children in FLDS prairie dresses and modest clothing gathering nuts at the Southern Utah Pecan Ranch outside of Hurricane.

A Labor Department investigation ensued. Investigators discovered the harvest was supervised by Paragon, which works as an employment agency. The Labor Department fined Paragon $10,395 in 2006 for using 12- and 13-year-old boys as construction workers. About a year later, it was fined $5,280 for a 16-year-old working in roofing operations.

In the pecan harvest, investigators obtained a voicemail that the Labor Department later contended was sent to Jeffs followers in Hildale, Utah, and Colorado City, Ariz.

"Good afternoon, this is a message from the Bishop's Office," according to a transcript in the federal lawsuit. "This is a call for all schools to take the rest of the week off of school to help with the nut harvest."

Court filings from the Labor Department say as many as 1,400 women and children participated in the harvest. A filing from a Department of Labor office in Salt Lake City says FLDS families were not paid for their services. Instead, they kept half the nuts and the other half remained with the ranch.

The ranch sold the nuts and 70 percent of gross proceeds go to Paragon, under the contract between the two, according to a court filing.

In a deposition, Paragon's owner, Jessop, said the check his company received from the ranch was deposited in a church account.

While the Labor Department may be done with its "subpoena enforcement litigation," its lawsuit in Salt Lake City remains pending. The Labor Department had been trying to force Lyle and Nephi Jeffs to sit for new depositions, and it was unclear if those had depositions had occurred.

The appeals of the fines will proceed in an administrative court. Further information on the appeals was not available Tuesday.

Twitter: @natecarlisle