In a written statement Friday, Sigma Phi Epsilon said it suspended the Alpha Chapter at the University of Mississippi and the chapter voted to expel all three men and turn over their identities to investigators.
Police on Sunday found a noose tied around the neck of the statue, along with an old Georgia flag with a Confederate battle emblem in its design. The design has since been updated to exclude the emblem.
The FBI said Friday it planned to expand the investigation for potential violations of federal law.
The University of Mississippi wants to question the three white students in connection with the vandalism of the statue.
But attorneys for the three students aren't allowing them to be questioned without arrest warrants. The three have not yet been identified.
University spokesman Danny Blanton said Friday the school's findings have been turned over to the district attorney's office. Blanton said the university will also proceed with internal disciplinary action through a judicial panel that consists of both faculty and students.
District Attorney Ben Creekmore did not immediately respond to a message left by The Associated Press. However, he told WMC-TV in Memphis that criminal charges would be difficult.
Creekmore said investigators and prosecutors have looked into several misdemeanors as possible charges, but he said criminal charges were unlikely by his office because the statue was not physically damaged, and the suspects did not appear to be trespassing.
He said federal investigators could opt to bring charges if they saw fit. Creekmore said if new information comes to light, his office could revisit the issue.
FBI spokeswoman Deborah Madden said the agency is continuing to assist in the investigation.
The Ole Miss Alumni Association is offering at $25,000 reward for information leading to an arrest. University Police Department Chief Calvin Sellers said the reward offer gave police some good leads in the case.
When Meredith tried to enter Ole Miss in fall 1962, Mississippi's governor tried to stop him. That led to violence on the Oxford campus.
U.S. Attorney General Robert Kennedy sent 500 U.S. marshals to take control and days later, Meredith was allowed in the school. Though he faced harassment during his time at the school, he graduated with a degree in political science.
(ABC7 News contributed to this report)