Iraq, which was covered in the previous seven-nation order, has been removed from the new list after agreeing additional visa vetting measures.
The new order, which includes a 120-day ban on all refugees, takes effect on March 16 to limit travel disruption.
The previous order, which was blocked by a federal court, sparked confusion at airports and mass protests.
Citizens of Iran, Libya, Syria, Somalia, Sudan and Yemen, the other six countries on the original list, will once more be subject to a 90-day travel ban.
Iraq was taken off the banned list in the original order – which was issued on January 27 – because its government has boosted visa screening and data sharing, White House officials said.
The new directive says refugees already approved by the State Department can enter the United States; it limits the number allowed in to 50,000 for the year.
The order also lifts an indefinite ban on all Syrian refugees.
Green Card holders from the named countries will not be affected by the new order.
The new order also does not give priority to religious minorities, unlike the previous directive.
However, critics of the Trump administration had argued that was an unlawful policy showing preference to Christian refugees.
Secretary of State Rex Tillerson, Homeland Security Secretary John Kelly and Attorney General Jeff Sessions held a joint news conference on March 6 to discuss the new directive.
Rex Tillerson the order was meant to “eliminate vulnerabilities that radical Islamic terrorists can and will exploit for destructive ends”.
Jeff Sessions said that, according to the FBI, more than 300 people who entered the US as refugees are under investigation for potential terrorism-related offences.
He said three of the countries were state sponsors of terrorism.
The other three, the top prosecutor said, had lost control of territory to militants such as ISIS or al-Qaeda.
John Kelly added that unregulated and unvetted travel was putting national security at risk.
He told reporters: “Our enemies will exploit our freedoms and generosity to harm us.”
John Kelly said the US cannot tolerate “malevolent actors using our immigration system to take American lives”.
None of the cabinet secretaries took any questions after the press conference.
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