“It is time for the Transitional Government of South Sudan to stop taking advantage of the United States,” said Rubio.
“Every country must accept the return of its citizens in a timely manner when another country, including the United States, seeks to remove them,” he added.
It comes as fears grow that South Sudan may again descend into civil war.
On 8 March, the US ordered all its non-emergency staff in South Sudan to leave as regional fighting broke out, threatening a fragile peace deal agreed in 2018.
South Sudanese in the US were previously granted Temporary Protected Status (TPS), which allows them to remain in the US for a set period of time.
TPS for South Sudanese in the US had been due to expire by 3 May.
South Sudan, the world’s newest nation, gained independence in 2011 after seceding from Sudan.
But just two years later, following a rift between President Salva Kiir and Vice-President Riek Machar, the tensions erupted into a civil war, in which more than 400,000 people were killed.
A 2018 power-sharing agreement between the two stopped the fighting, but key elements of the deal have not been implemented – including a new constitution, an election and the reunification of armed groups into a single army.
Sporadic violence between ethnic and local groups has continued in parts of the country.
Since returning to office, the Trump administration has clashed with international governments over deportations of their nationals from the US.
In January, Colombian President Gustavo Petro barred two US military flights carrying deported migrants from landing in his South American country.
Petro relented after Trump promised to place crippling tariffs and sanctions on Colombia.
One of the most famous South Sudanese citizens currently in the US is Duke University star basketball player 18-year-old Khaman Maluach.
A spokesman for the university said on Sunday the school is “aware of the announcement… regarding visa holders from South Sudan”.
“We are looking into the situation and working expeditiously to understand any implications for Duke students.”
Maluach, who played for the South Sudanese Olympic basketball team last summer, spent much of his life in Uganda after fleeing his violence in his homeland as a child.
The first-year student – whose Duke team was eliminated from the national championship tournament Saturday night after losing in the semi-finals to the University of Houston – is widely expected to join the ranks of the NBA after graduation.
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Source: BBC
