Senior administration officials said a review of Sudan's cooperation with their national security concerns and information-sharing showed that it was appropriate to remove them from the list.
The new restrictions will be phased in over time, officials said, and the restrictions will not affect anyone who already holds a US visa.
The original travel ban was created as a temporary measure, designed to give officials a few months to assess the vetting of visa applicants and what information other countries could and couldn't provide.
"The restrictions either previously or now were never, ever ever based on race, religion, or creed," said one senior administration official. "Those governments are simply not compliant with our basic security requirements."
The original version, signed as an executive order in January, blocked citizens of seven majority-Muslim countries - Iraq, Iran, Sudan, Somalia, Libya, Yemen and Syria - as well as all refugees across the globe.
When that measure was blocked in court, Trump signed a revised order removing Iraq from the banned list and only barring the issuance of visas to citizens of the six remaining countries and all refugees.
The second order, too, was blocked by judges, but the Supreme Court in June allowed it to go into effect with a significant caveat. The administration, the court said, could not block those with a "bona fide" connection to the United States, such as family members or those with firm offers of employment, from entering the country.
The ban on citizens of the six countries was to last 90 days; the ban on refugees was to last 120 days. The refugee ban is set to expire Oct. 24, and it was not immediately clear what impact the new restrictions might have on it.
The Supreme Court has scheduled arguments for October 10 on whether the measure, at its core, is legal. It is unclear how any new restrictions might affect that case, and it is possible that they could spark fresh legal challenges.
Many countries, officials said, already met U.S. requests - using secure biometric passports, for example, and willingly passing along terrorism and criminal-history information. Others agreed to make changes and share more data. But some were either unable or unwilling to give the United States what it needed, officials said.
Citing an attack in London earlier this month, Trump seemed to call for an expansion of the travel ban, writing on Twitter, "The travel ban into the United States should be far larger, tougher and more specific-but stupidly, that would not be politically correct!"