"The president's executive orders remain in place -- prohibited travel will remain prohibited, and the US government retains its right to revoke visas at any time if required for national security or public safety," the agency said in a statement.
"The president's executive order affects a minor portion of international travelers, and is a first step towards reestablishing control over America's borders and national security."
US District Judge Ann Donnelly granted the stay late yesterday, writing in her decision that sending those travelers back to their home countries following Trump's order exposes them to "substantial and irreparable injury."
Trump's executive order, signed Friday, suspends the arrival of refugees for at least 120 days and bars visas for travelers from seven Muslim majority countries for the next three months.
Judge Donnelly's ruling -- which did not touch on the constitutionality of Trump's crackdown -- coincided with a wave of anger and concern abroad, including among US allies, and rallies at major airports across the United States.