Annie Stevens, UVM's associate vice president for student and campus life, called the survey "incredibly offensive and inappropriate," saying it asks participants if they could rape someone, who would it be.
Sigma Phi Epsilon has been suspended temporarily during the investigation.
The school is investigating where the survey came from, who saw it and how it was used, officials said.
A student reported the survey to UVM officials, who notified police.
Sigma Phi Epsilon was already on social probation for alcohol violations, according to CBS affiliate WCAX. The station reported that the fraternity's survey starts with typical questions: name, major, favorite memories.
But, the final question drew the eye of the UVM administration. It reads: "If I could rape someone, who would it be?"
Student blogs claim a new member of Sigma Phi Epsilon accidentally emailed the survey - rather than his assignment - to a teaching assistant. One blog also alleges a fraternity brother has been accused of rape.
So-called "Greek life" encompasses about 8 percent of students at the northern Vermont campus.
Members of the Burlington fraternity would not comment on the allegations, said Justin Adelman, vice president of recruitment. The national chapter of the fraternity located in Virginia has been notified of the allegations.
A Burlington feminist organization FED UP Vermont and other groups on the UVM campus posted an online petition seeking to shut down the fraternity and planned a press conference to speak out against "rape culture and sexism" on Thursday at noon on the steps of the UVM library.