Pipkins told Schad that Harbaugh, associate athletic director Jim Minick and trainer Paul Schmidt asked him about 10 times over a two-month span to sign a medical form that would have put an end to his career.
Pipkins appeared in six games and recorded nine total tackles last season after recovering from a torn anterior cruciate ligament in his left knee.
He told ESPN that he suffered a concussion this spring but that he had received clearance from a neurologist. Pipkins also said he suffered another concussion when he was a freshman with the Wolverines.
He told ESPN that he feels "healthy and ready to play" and that he does not want to sign the form. Pipkins also said that he has knowledge of at least one other teammate who has been told to "get healthy by a July 1 deadline or sign a medical to retire."
Pipkins said doctors initially told him he has some arthritis in the knee but that he should not be disqualified from competition. But as pressure continued from others within the program to sign the medical form, he was sent by Michigan back to his knee surgeon, who then recommended he rest his body for six months.
"After consulting with our medical team, we do not think it is in Ondre's best interest as it relates to his health and welfare to play football, short or long term," Harbaugh said in a statement given to ESPN on Friday. "He remains on full scholarship and counts toward the 85-scholarship limit in pursuit of graduation from the University of Michigan."
According to Pipkins, Harbaugh said he wanted "to make sure you graduate from Michigan," and the coach did not plan to invite Pipkins to fall camp due in part to medical concerns. The lineman added that Harbaugh said he did not believe he would be drafted into the NFL for medical reasons.
Pipkins arrived at Michigan as a five-star recruit in the class of 2012, according to Rivals.com. He appeared in 18 games and compiled 14 total tackles over two seasons as a reserve defensive tackle.
Pipkins told ESPN that Michigan informed him this week that he could contact schools regarding his desire to transfer.
"All I want to do is play football," Pipkins said, according to ESPN. "I tried to finish my career at Michigan but I wasn't given the chance."