Secretary of State Marco Rubio said Friday that a federal court order requiring the US government to maintain custody of carriers in flights intended for South Sudan would cause “significant and irreparable damage to US foreign policy.”
The Trump administration said late Friday that US District Judge Brian Murphy, Massachusetts, could challenge an order sent to its own country after the deportation flight violated his previous April injunction.
“The Justice Department believes this situation urgently requires judicial intervention to restore full powers to implement President Trump's foreign policy,” a US Department of Justice official told Fox News Digital.
Rubio said the order already complicates diplomacy with Libya, South Sudan and Djibouti, and presents a serious threat to the president's Article 2 authority to implement foreign policy.
Federal judge orders the Trump administration to track out ousted immigrants to South Sudan
The Trump administration filed two court documents late Friday after a judge said the deportation flight had violated an earlier injunction. (AP Photo/Jose Luis Magana)
Rubio said in his filing that the court's order “had already quiet diplomatic efforts and exacerbated Libya's internal political and security sector.”
The order also “detects the efforts to quietly restructure productive cooperation with Juba,” the South Sudan capital said.
Before the court's intervention, Rubio said the South Sudanian government refused to accept South Sudanian people, but has since “taken steps to work more cooperatively with the US government.”
DHS reveals crimes from migrants deported to South Sudan as judges threatened to order return
Third, Rubio said the order “will be strategically located on the Horn of Africa” and “causing harm” along with the only US military base on the African continent.
The country is temporarily detained at a US Navy Base in Djibouti.

Deportation flights headed to Guatemala in January. (AP Photo/Christian Chavez, File)
In its second submission, the administration asked the court to “review” the order and “very burdensome requirements.”
“According to this court's order, the US government is currently detaining dangerous offenders in sensitive places without clearly knowing when, how and where this court will tolerate release,” the filing said.
A judicial suspension of deportation is putting us at risk of foreign policy, official claims from Career State University
“This development has given unacceptable and burdensome constraints to the President's ability to carry out his Article 2 powers, including his power to command the military, manage relations with foreign countries and enforce immigration authorities in our country.”
Denner claimed that “received the benefit of the full process under US law and was legally removed from the country,” and called for a stay if not a reconsideration of the order.
“These offenders simply stated that they were afraid to remove them in South Sudan to receive the other procedures necessary in the court's injunction on April 18, 2025,” the administration wrote. “Aliens did not. Therefore, DHS tried to remove these aliens who committed the most condemning violations of our country's laws, where they no longer pose a threat to the United States.”

Secretary of State Marco Rubio said Friday that a court order requiring the US government to maintain custody of carriers in flights intended for South Sudan would cause “severe and irreparable damage to US foreign policy.” (AP Photo/Jose Luis Magana)
Departing from Texas earlier this week, there are eight immigrants from Myanmar, Laos, Vietnam, Cuba, Mexico and South Sudan.
Murphy issued the ruling Tuesday night after immigrant lawyers from Myanmar and Vietnam accused Trump administration of illegally deporting him to a third-party country. They argue that there are court orders that prevent such removal.
Murphy's ruling stated that the government “should maintain custody and control of class members currently being taken to South Sudan or other third countries, and ensure the actual feasibility of return if the court finds such removal is illegal.”
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Rubio announced in April that the US would cancel visas held by South Sudan's passport holders, with no other visas being issued and “due to the South Sudan transitional government's failure to accept a timely return of citizens who have been re-released.”
The United States has third party deportation agreements with the most notable number of countries, El Salvador, which has accepted hundreds of Venezuelan contingents from the Trump administration.
Brooke Singman of Fox News contributed to this report.