WASHINGTON — In announcing the United States’ annual list of the world’s worst human rights violations, Secretary of State Mike Pompeo this past week singled out South Sudan and Nicaragua for government-sanctioned atrocities against their own people.

Over the past year in South Sudan, Mr. Pompeo said, “military forces waged sexual violence against civilians based on their political allegiances and their ethnicity.” In Nicaragua, he said “when citizens peacefully protested Social Security benefits, they were met with sniper fire.”

But the Department of Homeland Security has sought to limit the number of immigrants who left South Sudan or Nicaragua for safety, seeking to temporarily live and work legally in the United States.

The apparent contradiction shows the Trump administration’s competing priorities and how they affect foreigners facing government corruption and violence.

Even as homeland security has sought to tighten American borders and strictly enforce immigration laws, the State Department is highlighting some of the very systematic abuses that have sent people fleeing to the United States.

That “perfectly illustrates the unfairness inherent in this administration’s approach to temporary protected status,” said Ahilan Arulanantham, the senior counsel at the American Civil Liberties Union of Southern California, referring to a program that gives immigrants short-term residency. He is representing plaintiffs in a lawsuit against the administration’s efforts to pull those protections from immigrants.

Homeland security officials defended its approach to limit — and in many cases revoke — temporary protected status on a country by country basis.

The policy, first enacted in 1990, allowed people from countries suffering from war, natural disasters, epidemic or “extraordinary and temporary conditions” to live and work in the United States until their homelands stabilized. The Trump administration has sought to restrict it, saying the protections have allowed immigrants to gain long-term residency.

One homeland security official said the policy was never intended to give permanent relief to immigrants, who could otherwise apply for refugee grants or benefit from American political pressure or direct intervention on their home countries. The official spoke on the condition of anonymity to discuss a policy that is being challenged in court.

An estimated 2,500 Nicaraguans are living in the United States under temporary protected status and have been ordered to leave, adjust their immigration status or face deportation. They have been given a reprieve as a federal court in California considers their case, along with immigrants from El Salvador, Haiti, Sudan, Honduras and Nepal who are also challenging the administration’s deportation order, which they say is racially motivated.

Temporary protected status was first opened to Nicaraguans in 1999 after the devastation caused by Hurricane Mitch, and extended for years afterward. As part of its decision to withdraw the protections, homeland security officials concluded that conditions are now safe enough in Nicaragua for the immigrants to return.

The State Department report, however, found that clashes in Nicaragua that began last April between the police and protesters have so far killed 325 people and injured 2,000 more. Hundreds have been illegally detained and tortured, and more than 52,000 exiled, the report found. Some of those who were detained were raped by government officials; lesbian, gay, bisexual and transgender as well as indigenous people were attacked.

“Human rights deteriorated markedly during the year,” the report on Nicaragua concluded.

The disparity between the two agencies’ assessments of South Sudan is slightly blurrier.

This past week, Kirstjen Nielsen, the homeland security secretary, approved a limited extension for immigrants from South Sudan, allowing those who were already in the United States before January 2016 to remain for another 18 months. It was the second time since temporary protected status, commonly referred to as T.P.S., was granted to South Sudan in 2011 that the United States limited its extension to only some of the immigrants. (The first, more limited extension of the temporary protections was granted to the country in 2017.)

Ms. Nielsen “determined the ongoing armed conflict and extraordinary and temporary conditions that support South Sudan’s current designation for T.P.S. continue to exist,” the Department of Homeland Security said in a statement.

But the protections did not extend to those from South Sudan who came to the United States after January 2016. Warring factions in South Sudan reached what the United Nations has described as a fragile peace agreement in 2018, after five years of ethnic violence in South Sudan.

That has infuriated pro-immigration advocates who said hundreds of immigrants who had hoped to win temporary legal residency, and are already in the United States, now face imminent deportation to South Sudan.

“While the warring parties were able to come to a peace agreement, many people are still being displaced from their homes due to fighting and insecurity and there is substantial work to be done to address the longtime suffering of the South Sudanese people,” said Martin Omukuba, who oversees South Sudan policy at the International Rescue Committee, a humanitarian aid group.

The State Department described a range of atrocities in South Sudan throughout 2018 — many at the hands of government officials or security forces.

They included “rape and gang rape employed as a weapon of war, arbitrary detention and torture, enforced disappearances, explosive remnants of war, forced displacement, the mass destruction of homes and personal property, widespread looting, and use of child soldiers,” the department’s report found.

At least 382,000 people have been killed in the conflict in South Sudan, according to the report, which cited figures from the London School of Hygiene and Tropical Medicine.

There is a history of tension between the State Department and the Department of Homeland Security over ending or otherwise limiting temporary protected status for immigrants.

In a 2017 email exchange obtained by the A.C.L.U., a senior diplomat raised concerns over how homeland security officials would announce the end of the protections for immigrants from Sudan.

The diplomat, Paul Sutphin, then a senior adviser for the State Department’s special envoy to Sudan and South Sudan, wrote that language about the policy that was being prepared for publication in the Federal Register might encourage “the Sudanese government to take actions that could exacerbate the ongoing armed conflicts in South Sudan.”

Mr. Sutphin said the Sudanese government could view the language as a “green light” to force displaced people to “deadly conflict-affected areas” and pushed homeland security officials to make clear that there was still an internal conflict in South Sudan.

Mr. Sutphin did not return requests for comment.

In a subsequent email, another State Department official said diplomats were caught off guard by the Department of Homeland Security’s announcement in September 2017 that it would end temporary protected status for immigrants from Sudan.

The State Department report released this week found that in Sudan last year, “human rights issues included unlawful or arbitrary killings, forced disappearance, torture and arbitrary detention.”



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