The filings come after the Texas Health and Human Services Commission sought an injunction in Dallas on Wednesday seeking to stop IRC from bringing six Syrians to the city, citing security concerns.
According to the court filings, 12 Syrian refugees bound for Texas arrived in New York on Thursday and Friday.
Texas "has made no showing that these refugees pose any threat, much less an imminent one, to the safety or security of Texas residents or any other Americans," the Obama administration told the court.
Joining the defense of the International Rescue Committee is the American Civil Liberties Union, which says Texas cannot veto the resettlement of refugees who are already approved to enter the U.S. The civil rights organization accuses Texas of discrimination and says a ruling in the state's favor would set a troubling precedent.
Texas is the first U.S. state to ask a federal court to block the arrival of Syrian refugees following the deadly attacks in Paris in November, and its lawsuit comes two weeks after Gov. Greg Abbott ordered resettlement organizations in Texas to stop accepting Syrian refugees due to security concerns.