"This week alone, over 800 refugees were set to make America their new home", the Geneva-based UNHCR said in a statement.
The IOM and the UNHCR "hope that the United States will continue its strong leadership role and long tradition of protecting those who are fleeing conflict and persecution", the statement said.
An estimated 20,000 refugees in "precarious circumstances" would have been resettled to the United States during the 120 days covered by the suspension announced last Friday, the U.N. High Commissioner for Refugees (UNHCR) said in a statement.
The executive order plans to cut that number to 50,000.
"The longstanding policy has offered a double win: first by rescuing some of the most vulnerable people in the world, and second by enabling them to enrich their new societies".
The two Geneva-based agencies said they are committed to working with the new administration of United States towards a shared goal of ensuring safe and secure resettlement programmes.
"We have gotten assurances from the U.S. mission that UN staff members from those seven countries listed, who have valid G4 visas, will be allowed to come in the United States for their work", Dujarric said. It also imposed a 90-day ban on entry to the U.S. from seven Muslim-majority countries.
Trump justified the moves as necessary to prevent "radical Islamic terrorists" from entering the US.
US President Donald Trump on Friday signed an executive order suspending all visa applications from Iraq, Syria, Iran, Sudan, Libya, Somalia and Yemen for at least 90 days.
Help Refugees, a British charity working across camps in northern France, Greece and the Middle East, said news of Mr Trump's order was "devastating".
UNHCR estimates, based on average monthly figures for the last 15 years, that 20,000 refugees in precarious circumstances might have been resettled to the United States during the 120 days covered by the Order.
"The reality is that the US refugee resettlement program saves lives - namely of women and children under 12, who make up 67 percent of the Syrian refugees in the USA - while helping to ensure the safety of our country".
Before being approved for resettlement by American authorities, refugees undergo an in-depth process that includes up to 36 months of vetting - including biometric screening - by 12 to 15 government agencies including the Department of Homeland Security and intelligence services.