Campus officials said they were taking the threat of violence seriously and, as a precaution, canceled the student meeting.
The threats were not specific, but university police have increased their presence on campus and alerted students and faculty.
Campus officials are calling on students and faculty to report any suspicious activity.
"The safety of our campus and its students, faculty and staff is and will always be our absolute, utmost concern," Chancellor Howard Gillman said in a statement. "There is no gray area when it comes to threats of violence; they will not be tolerated, and we cannot allow our community to be put at risk."
The controversy over the flag display arose last week when the legislative council for the Associated Students approved a resolution calling for the removal of the American flag and other flags from a lobby.
The resolution read: "The American flag has been flown in instances of colonialism and imperialism."
The decision went viral, with students and faculty members denouncing the action.
But that action was vetoed Saturday by the executive cabinet of the student government. The action was expected to come before the entire student government board Tuesday.
Student government leaders supported the decision to cancel Tuesday's meeting, and Gillman condemned the threats.
"Regardless of your opinion on the display of the American flag, we must be united in protecting the people who make this university a premier institution of higher learning," he said. "Our campus must be a place for safe and civil discourse. We continue to call on everyone to condemn all harassment and threats of violence."