The president's statement came as the US Justice Department said it would join the FBI's preliminary inquiry to determine whether the man accused in the Chapel Hill shooting on Tuesday broke any federal laws, including hate crime laws.
"No one in the United States of America should ever be targeted because of who they are, what they look like, or how they worship," Obama said in a statement, offering his condolences to the victims' families.
The families had called on Obama to insist that federal authorities investigate whether the murder suspect, 46-year-old paralegal student Craig Stephen Hicks, was motivated by hatred toward the victims because they were Muslim.
Police seized more than a dozen firearms and a large amount of ammunition from his home, according to search warrants filed on Friday, WRAL-TV reported.
Newlywed Deah Shaddy Barakat, 23, a University of North Carolina dental student, his wife, Yusor Mohammad Abu-Salha, 21, and her sister, Razan Mohammad Abu-Salha, 19, a student at North Carolina State University, were killed in a condominium about two miles (three km) from the UNC campus.
According to the warrants, a friend of the victims' stopped police and directed them to the condo, where authorities found Barakat dead and bleeding from his head in the front doorway, the television station reported.
One of the sisters was found in the kitchen and the other in its doorway, according WRAL-TV.
On Thursday, Turkish President Tayyip Erdogan criticized Obama and other US leaders for their silence about the incident, which has garnered international attention and left some US Muslims feeling concerned about their safety, Reuters reported.