The Trump administration will temporarily delay processing of most refugees from 11 countries identified as high-risk, while resuming refugee admissions for other countries.
Most of the affected countries are in the Middle East and Africa.
The administration also will place on hold a programme that allows for family reunification for some refugees resettled in the United States, according to a Trump administration memo sent to Congress yesterday.
The resettling of so-called following-to-join refugees will resume, according to the memo, once screening "enhancements have been implemented".
US officials said the changes were aimed at protecting US national security, but refugee advocates said they amounted to a de facto ban on refugees from the 11 countries and were unnecessary, since refugees are already heavily vetted.
The changes come at the close of a 120-day ban on most refugees ordered by President Donald Trump to allow a review of vetting processes.
The 120 days ended yesterday and Mr Trump issued an executive order allowing the general resumption of the US refugee programme.
The memo expressed concerns about admitting refugees from the 11 countries and said the government would conduct a 90-day review "to determine what additional safeguards, if any, are necessary to ensure ... the security and welfare of the United States".
Mr Trump took office in January with a goal of sharply cutting refugee admissions, in line with promises he made during the 2016 election campaign.
He quickly issued temporary bans on refugees and travellers from several Muslim-majority countries, which were challenged in court.
Opponents of the bans argued that the policies were aimed at barring Muslims from the United States.
The administration has denied any intent to discriminate and says its travel ban and security changes are meant to protect the United States from terrorist acts.
The Supreme Court yesterday dismissed the last remaining challenge to an earlier version of Mr Trump's travel ban.