"These additional security measures will make it harder for bad actors to exploit our refugee program, and they will ensure we take a more risk-based approach to protecting the homeland," Homeland Security Secretary Kirstjen Nielsen said in a statement.
"The United States must continue to fulfill its obligation to the global community to assist those facing persecution and do so in a manner that addresses the security of the American people," she said.
The new measures will include additional interviews of applicants' family members and close scrutiny of potential ties to organized crime, senior U.S. officials said in a conference call with reporters Monday.
U.S. standards for refugee acceptance are already considered some of the toughest in the world, and the process typically takes one to two years. Critics of the administration view the additional screening measures as part of President Trump's broader goal of limiting all forms of immigration to the United States, especially from majority-Muslim countries.
The Trump administration has refused to identify the 11 nations it considers high-risk, citing "law enforcement sensitivities." But officials with knowledge of the list say it includes Egypt, Iran, Libya, South Sudan, Yemen, Sudan, Iraq, Mali, North Korea, Somalia and Syria.
All but North Korea and South Sudan are majority-Muslim.
A senior U.S. official insisted Monday that the high-risk determination for the 11 nations "has nothing to do with religion."
When he campaigned for president, Trump said that he would ban Muslims from entering the United States and that violent extremists could be slipping into the country with a "massive inflow of refugees."
Once in office, Trump froze refugee admissions and capped the number the United States would accept at 45,000 per year, the lowest total since the Refugee Act was created in 1980.
The United States resumed admitting refugees in October, but the White House ordered the DHS to continue tightly restricting applicants from 11 nations it deemed the most risky, saying it needed an additional 90 days to further assess screening procedures.
Making good on his campaign promises, Trump called for an "extreme vetting" system to make sure "radical Islamic terrorists" were not sneaking in with those fleeing wars, persecution and violence.
Senior officials said U.S. screeners will recommence interviews with high-risk applicants during the second quarter of 2018 and have resumed processing applications from those countries.
The enhanced security measures will also increase information sharing among the U.S. agencies tasked with vetting refugee applicants, according to administration officials. The high-risk list will be reviewed every six months, and countries could be added or removed based on evolving assessments of security threats to the United States.
In December, a federal judge in Seattle partly blocked the administration's directive on the 11 nations, ordering the DHS to resume processing applicants who have family members already living in the United States.
The refugee screening measures are separate from the Trump administration's broader attempt to ban travelers from six Muslim-majority nations.
In December the Supreme Court granted the administration's request to fully implement a revised order barring those travelers, saying it could be enforced while legal challenges unfolded in lower courts.