Under Secretary Tom Vilsack, shown, the U.S. Department of Agriculture has settled large class-action civil rights lawsuits brought by Native American and black farmers and ranchers. (Craig Lassig/European Pressphoto Agency)

Native American farmers asked a federal judge Thursday to fix the “monumental” failure of a landmark civil rights settlement that has left $380 million — more than half the total — unclaimed after the U.S. government agreed to pay the farmers for years of official discrimination.

The government in 2010 committed $680 million to resolve a class-action lawsuit by thousands of Native American farmers and ranchers. The suit filed in 1999 alleged that the Agriculture Department discriminated against Native Americans in loan programs from 1981 to 1999.

Only about 3,600 successful claimants came forward after the settlement, not the more than 10,000 expected. Those who filed claims received roughly $180 million plus $60 million in tax payments on their behalf, not counting other relief on farm loan debt. About $60 million went to ­attorneys.

But that left unclaimed the hundreds of millions set aside for the settlement and launched a battle over how to handle those funds.

“The scope of this failure is monumental; the reasons for it remain unclear,” U.S. District Judge Emmet G. Sullivan of the District wrote in July, calling the result a “cautionary tale” in class-action law.

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Experts said the inability to distribute money to more aggrieved farmers could track to several factors: the department’s failure to keep records of applicants who previously had been denied loans, a history of skepticism in Indian country about federal promises and the hurdles of reaching poor and isolated Native Americans in remote areas who — based on previous calculation models used in litigation — were believed to have been engaged in agriculture.

Sullivan rejected competing proposals last summer to split the untapped $380 million among class recipients — which the government opposed — or to distribute the money over 20 years through a trust led by Native Americans to charities selected by class attorneys. The dispute pit class members against one another and against lawyers who represented the overall group.

Instead, Sullivan called for new talks.

The original settlement cannot be changed after April 28 without agreement on what to do with the leftover funds, said John G. Dillard of Olsson Frank Weeda Terman Matz, a lawyer for lead plaintiff Marilyn Keepseagle, a North Dakota Sioux rancher.

Under those original terms, now criticized by all sides, what was expected to be a small amount of leftover money would have to be distributed in equal shares to nonprofit groups chosen by class attorneys.

Sullivan said that because of the larger amount left unclaimed that option “could be viewed as both unjust and inefficient.”

Attorneys for Keepseagle, the class and the department produced a new agreement in December, to award successful claimants an additional $21,275 in cash and tax payments in their behalf — about $77 million in all — atop the $50,000 apiece most received initially.

Another $38 million would go to nonprofit groups chosen by class counsel and the rest, would endow a Native American-led trust that could use its discretion to distribute money to nonprofit groups — an arrangement that could create the largest U.S. philanthropic institution to serve Native American farmers and ­ranchers.

About 70 percent of 300 written comments filed with the court, and several of nearly 100 people who filled Sullivan’s courtroom Thursday, opposed the proposal. Those who objected include individuals who had tried to collect through the settlement but were denied and those who had never filed and were left out altogether.

Three of four named class representatives, including Keepseagle and Claryca Mandan, a North Dakota rancher with the Hidatsa tribe, said that they believed that they had no choice but to accept the deal that includes some added payment to people like them but also creates the large trust and donations to charities.

“It is with a heavy heart and great reluctance we accept this meager amount,” Mandan said. “It was too much to risk not getting any money at all.”

Another representative, Keith Mandan, Claryca’s ex-husband, opposed it. Keith Mandan agreed with William H. “Billy” Smallwood Jr., a successful Choctaw claimant from Antlers, Okla., who filed a new lawsuit this week challenging the distribution of funds to “undeserving third parties” — including charities with no track record formed just to capture the taxpayer-funded windfall — at the expense of proven victims of discrimination.

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Dillard said that he was “cautiously optimistic” the change would be approved, because time to make changes was running out for the court and for many aging farmers.

Of nine original class representatives, Keepseagle is now 78, four others are deceased, and one has dementia, Dillard said. “There’s real interest in going ahead and resolving this matter now,” he said.

Lead class attorney Joseph Sellers of Cohen Milstein Sellers & Toll said the result was a compromise by all sides to serve “a community that has suffered enormous poverty over centuries and has extraordinary financial needs.”

Sellers said that he hoped the dispute over the leftover money would not distract from the case’s achievements, which in addition to funds included a systematic review of farm loan rules and the creation of a Native American advisory council for the department.