The quota of 50,000 was initially set by President Donald Trump as part of his travel ban executive order in January, but was shelved for several months as the legality of the order was contested in the US court system.
Last month, when the Supreme Court upheld elements of the ban, the quota was reinstated.
However, the administration modified its policy to reflect the court's ruling, which stated that individuals with a "bona fide relationship with any person or entity in the United States" should be allowed entry into the country.
Refugee applicants overseas with a "credible claim" of such a bona fide relationships are still being interviewed and vetted, a spokesperson for the Department of Homeland Security told CNN Tuesday, though most of them will not travel to the US until the next fiscal year because of length of the vetting process.
A State Department spokesperson confirmed that the US had reached the 50,000 cap and stated that "beginning July 13, only those individuals who have a credible claim to a bona fide relationship with a person or entity in the United States will be eligible for admission through the US Refugee Admissions Program."
The administration's quota covers the current fiscal year, which began on October 1, 2016, and ends on September 29.
The Immigration and Nationality Act gives the President the authority to set refugee admissions targets, in consultation with Congress. Former President Barack Obama initially set a target of 110,000 refugees for the current fiscal year -- a goal that was panned by then-candidate Trump.
"They can't be properly vetted," Trump said of the refugees in an interview on Fox News at the time. "There's no way."
Days after taking office, Trump signed an executive order that banned all refugee admissions for four months, banned Syrian refugee admissions indefinitely, instituted the 50,000 cap and called for a broad review of vetting procedures.
Controversially, the order also prioritized refugees from persecuted religious minority groups, a move that was perceived by some as an effort to increase the number of Christians from the Middle East relative to Muslims.
In a statement Wednesday, Lutheran Immigration and Refugee Service (LIRS) -- one of nine approved US refugee resettlement agencies -- criticized the administration for its "historically and arbitrarily low cap."
"The pause on resettlement and restrictions on the number of persons who can enter our country as refugees will have an immediate effect on our ability to conduct the lifesaving work of providing safety and protection," said LIRS Vice President for Programs Kay Bellor.