The suit, filed by Patrick Dennehy Sr., seeks unspecified damages and names Baylor University, former coach Dave Bliss, school president Robert Sloan, former athletic director Tom Stanton and others associated with the program.
Dennehy disappeared in mid-June and his body was found in a field July 25. He had been shot twice in the head. Former teammate and roommate Carlton Dotson is in jail in Maryland, accused of murder.
According to the lawsuit, after getting no response over his concerns about improprieties within the school's basketball program, Dennehy Jr. decided it was his responsibility to expose "illegal activities within the athletic department."
"Shortly after making that decision, Patrick became the target of violent threats against his person and soon became fearful for his life," the lawsuit states. It said school administrators and the athletic department "again turned their backs on Patrick."
It also states that "Bliss's very presence at Baylor created an unsafe atmosphere for the student athletes and ultimately led to the murder."
"All of us are very shocked and stunned at the things that have happened," said Sloan Friday on CBS News' The Early Show. "I'm proud of the university for acting responsibly and acting according to our convictions and accepting responsibility."
The school launched an internal inquiry in July into possible NCAA violations after allegations surfaced of improper payments to players following Dennehy's death. Bliss and Stanton resigned Aug. 8.
Last week, secretly taped conversations were released in which Bliss could be heard trying to get players and assistant coaches to go along with a plot to say Dennehy was a drug dealer.
"It's hard to believe that Coach Bliss could have done the things that he's done," said Sloan.
The suit was filed in Houston, attorneys Daniel Cartwright and Richard Laminack said the lawsuit, to better ensure a fair forum because Baylor has "so much influence" in Waco.
The suit said the defendants' "acts and omissions directly (led) to Patrick's wrongful death." It seeks damages for physical pain, mental anguish, medical expenses, and compensatory damages and court costs.
Friends of Dennehy have said he told them both he and Dotson had been threatened, and that the pair obtained guns. Dennehy's family also said he told coaches he feared for his life.
Sloan said he could not comment on the lawsuit because neither he nor the school's attorneys had seen it.
He also told Early Show co-anchor Hannah Storm he had no plans to resign as president of the world's largest Baptist institution.
"Really, quitting is not the way to approach problems," he said. "I think you have to face problems squarely and at a place like Baylor, we face them with faith and courage and integrity and conviction and move on."