Ariel Agudio, Asha Burwell and Alexis Briggs, all 20, entered the pleas at an arraignment in Albany County Court on charges of third-degree assault and multiple counts of falsely reporting an incident, the Albany District Attorney's Office said.
They were released on their own recognizance.
A grand jury on Monday indicted the three women on the assault and false report charges.
Agudio and Burwell also pleaded not guilty to charges of harassment, while Agudio pleaded not guilty to three additional counts of attempted assault.
The State University of New York at Albany rallied behind the students, who are black, when they came forward with claims that a group of white men and women attacked them on January 30 in a confrontation on a city bus. Students held a rally
and university President Robert J. Jones said in a letter to students and faculty that he was "deeply concerned, saddened and angry about this incident."
Others came to their defense on social media using the hashtag #DefendBlackGirlsUAlbany. The People of Color Caucus issued a letter in support of them.
But university police said an investigation revealed that no one used racial epithets against the women. Instead, they assaulted another passenger and falsely reported the incident, authorities said.
"What happened on the bus was not a 'hate crime,'" University Police Chief Frank Wiley said in February. "The only person we heard uttering racial epithets was one of the defendants."
A tentative trial date was scheduled for September, the district attorney's office said.
The three women pleaded not guilty
in February to charges of assault and harassment. Two of them also pleaded not guilty to charges of falsely reporting the incident.
Agudio's lawyer, Mark Mishler, said in February the charges were unwarranted.
"It is also unfortunate that some in the media and public appear to have reached a conclusion as to what occurred in this incident without actually having the information needed in order to reach such a conclusion," Misher said in the statement.
"Ms. Agudio, an exemplary young woman and an excellent student who has never previously been in legal trouble, asks that people not rush to judgment in this matter."