Georgia Tech instructed students to stay inside during the unrest, but later announced that "the campus has been cleared of any threats".
After a vigil for Schultz Monday evening, a smaller group of about 50 protesters marched to the Georgia Tech Police Department.
Two police officers received minor injures and one of them was transported to Grady Memorial Hospital, a Tech spokesman said. Vincent Castillenti, Jacob Wilson and Cassandra Monden were all arrested and charged with inciting a riot and battery of an officer, according to the school. Stewart also accused the officer who opened fire of overreacting. In a cellphone video captured by an onlooker and obtained by CNN, at least two officers can be seen with their guns drawn as Schultz walks toward them.
The vigil for Scout Schultz was attended by almost 500 people, including Schultz's family, according to Georgia Tech President G.P. "Bud" Peterson.
The Pride Alliance said in a statement that it was "deeply saddened" by the incident, calling Mr Schultz "the driving force behind Pride Alliance for the past two years".
"While this is a heart-wrenchingly painful time for the entire Georgia Tech community, it is important to know that all of us here at Georgia Tech are committed to providing a safe and healthy, living and learning environment for all of our students, faculty and staff", he wrote.
In a statement released through Stewart, Schultz's family urged protesters to remain peaceful.
Authorities did not immediately release details about the protests.
As Schultz continues to advance, the tense confrontation ends with a gunshot fired by police, followed by the cries of the mortally wounded student.
The GBI said Monday Schultz had left behind three suicide notes and called 911.
Schultz was a fourth-year computer engineering student and president of Georgia Tech's Pride Alliance.
Schultz adds, "It looks like he's got, he's got a knife in his hand".
Miles says three suicide notes were found in Schultz's dorm room.
"I am grateful for our students, faculty, staff, campus leaders, and for our campus police".
William Schultz said his child was a great student with a 3.9 GPA and was on track to graduate early in December.
But Lynne Schultz told The Post that her child's mental health issues appeared to have been resolved and that friends reported Scout seemed fine in their fourth year at Georgia Tech.
A vigil to honor Schultz's life was scheduled to take place on the campus Monday night at 8 p.m.
Two people who ran past Shen had their faces covered with bandanas and were carrying what appeared to be "tools", he said.
"We believe many of them were not part of our Georgia Tech community, but rather outside agitators intent on disrupting the event", Peterson said.
A multi-purpose tool containing a knife was recovered at the scene.
Beck is on paid leave pending the outcome of the investigation, Georgia Tech said on its website. Cellphone video shows police telling Schultz, "Come on man, let's drop the knife" and "Nobody wants to hurt you, man". "The family now wonders where the narrative came from that Scout was wielding a knife and was a danger to officers", Stewart said in a statement. She told the Atlanta Journal-Constitution that Scout Schultz was suffering from depression and had attempted suicide by hanging in the recent past.