Obama notified Congress Tuesday he signed an order on the new waivers.
Republican senators said Obama's actions raised "significant concerns," and vowed to conduct a hearing to review them closely, CNN reported.
Obama threatened to veto the 2012 Defense Authorization Act, which include the detention language. However, a compromise was reached that required military custody for non-U.S. citizens suspected of being members of al-Qaida or its affiliates and who planned or carried out an attack against the United States or its coalition partners unless the president waives that provision.
Tom Malinowski of Human Rights Watch told CNN Obama's order Tuesday was "essentially a 3,450-word line-item veto, rendering the mandatory military detention provision mostly moot."
In a statement, Republican Sens. John McCain of Arizona, Lindsey Graham of South Carolina and Kelly Ayote of New Hampshire said the new waiver regulations may be the opposite of the intent of the legislation and "will require a hearing in the Senate Armed Services Committee."
The order waives the military requirement in situations when it would impede counter-terrorism cooperation, discourage a person from cooperating or confessing, hinder joint trials with co-defendants not in military custody; when a foreign government won't extradite a suspect if the United States puts the suspect in military custody; when a terror suspect is a legal permanent U.S. resident arrested in the United States or when an individual has been arrested by state or local law enforcement.
The order also states the attorney general can issue waivers for other reasons after consulting with senior national security officials.