Applications from 11 “high risk” countries will be delayed by a further 90 days to allow the administration to draw up even tighter restrictions.
The State Department said that admissions would be resumed on a case by case basis from citizens of the 11 countries, understood to be Egypt, Iran, Iraq, Libya, Mali, North Korea, Somalia, South Sudan, Sudan, Syria and Yemen.
During the election campaign, Mr Trump promised to slash refugee numbers as part of a pledge to take a far tougher line on immigration than the Obama administration.
Trump administration confirm new travel ban Trump administration confirm new travel ban
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He warned that thousands of refugees were being admitted without being screened, arguing that this was putting the US at risk.
"Thousands of refugees are being admitted with no way to screen them and are instantly made eligible for welfare and free health care, even as our own veterans, our great, great veterans, die while they're waiting online for medical care that they desperately need," Mr Trump said last October.
Opponents of the tighter controls said that the arrangements introduced by the Obama administration already imposed rigorous screening on refugees. The executive order suspending the refugee programme was signed by Donald Trump in March alongside his frequently challenged travel ban on citizens of six Muslim majority countries.
While the travel ban has been repeatedly overturned by the courts, the temporary refugee restrictions have been left largely untouched.
Although the refugee ban has been lifted, the number entering the US will fall dramatically with the Trump administration capping admissions at 45,000 over the next 12 months, less than half the limit imposed last year by the Obama administration.
Over the past few months, the global refugee crisis has intensified with the flight of more than 600,000 Rohingya Muslims from Myanmar to Bangladesh.
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