Rubio warns court order on South Sudan deportees harms US foreign policy

Secretary of State Marco Rubio said Friday that a federal court order requiring the U.S. government to maintain custody of deportees on a flight meant for South Sudan will cause “significant and irreparable harm to U.S. foreign policy.” 

The Trump administration late Friday filed two court documents after U.S. District Judge Brian Murphy of Massachusetts said the deportation flight violated his previous April injunction that allows deportees time to challenge an order to be sent to a country other than their own. 

“This Department of Justice believes that this situation urgently requires judicial intervention to restore President Trump’s full Article II authority to conduct foreign policy,” a U.S. Department of Justice official told Fox News Digital.

Rubio noted the order has already complicated U.S. diplomacy with Libya, South Sudan and Djibouti and presents a serious threat to the president’s Article II authority to conduct foreign policy. 

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Rubio said in his filing that the court’s orders had “already interfered with quiet diplomatic efforts and exacerbated internal political and security divisions” in Libya. 

The order also threatens to “derail efforts to quietly rebuild a productive working relationship with Juba,” the capital of South Sudan, he said. 

Rubio said before the court’s intervention that the South Sudan government had refused to accept a South Sudanese national but had since “taken steps to work more cooperatively with the U.S. government.” 

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Thirdly, Rubio said the order “causes harm” in Djibouti, which is “strategically located in the Horn of Africa” with the only U.S. military base on the African continent. 

The deportees are being temporarily held at a U.S. Naval base in Djibouti. 

In the second filing, the administration asked the court to “reconsider” its order and “highly burdensome requirements.”

“Because of this Court’s Orders, [the U.S. government is] currently detaining dangerous criminals in a sensitive location without clear knowledge of when, how, or where this Court will tolerate their release,” the filing said.

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“This development has put impermissible, burdensome constraints on the President’s ability to carry out his Article II powers, including his powers to command the military, manage relations with foreign nations, and execute our nation’s immigration authorities.” 

The deportees “enjoyed the benefit of full process under the laws of the United States and were lawfully removed from the country,” the filing claimed, calling for a stay if not a reconsideration of the order. 

“These criminal aliens needed only state that they had a fear of removal to South Sudan to receive the other procedures required by the Court’s April 18, 2025 injunction,” the administration wrote. “The aliens did not do so. Therefore, DHS attempted to remove these aliens — who have committed the most reprehensible violations of our nation’s laws — to a place where they no longer pose a threat to the United States.” 

The flight left from Texas earlier this week with eight migrants from Myanmar, Laos, Vietnam, Cuba, Mexico and South Sudan. 

Murphy issued the ruling Tuesday night after lawyers for the immigrants from Myanmar and Vietnam accused the Trump administration of illegally deporting their clients to third-party countries. They argue there is a court order blocking such removals.

Murphy’s ruling said the government must “maintain custody and control of class members currently being removed to South Sudan or to any other third country, to ensure the practical feasibility of return if the Court finds that such removals were unlawful.”

Rubio announced in April that the U.S. would revoke visas held by South Sudanese passport holders and no others would be issued, attributing the change to “the failure of South Sudan’s transitional government to accept the return of its repatriated citizens in a timely manner,” according to a statement posted on X at the time. 

The U.S. has third-party deportation agreements with a handful of countries, the most prominent being El Salvador, which has accepted hundreds of Venezuelan deportees from the Trump administration.

Fox News’ Brooke Singman contributed to this report.