The Tampa Bay Times obtained a copy of the letter and published parts of it on Friday.
The school’s athletic department said the case was first brought to its attention in January 2013 after a female student identified Winston as a suspect in the alleged sexual assault.
The athletic department questioned Winston and two other teammates who allegedly witnessed the incident, and all three said the sex was consensual.
Winston was investigated by the State Attorney's office, which decided not to pursue charges in December 2013, stating it could not guarantee that Winston could be convicted in court.
Winston went on to win the Heisman Trophy and lead the Seminoles to a national title.
"We did not want you to confuse our silence with idleness, a lack of caring or, as some have alleged, an institutional conspiracy to protect a star athlete," the letter said.
The U.S. Department of Education's Office for Civil Rights, under Title IX rules, requires schools to investigate any claims of sexual assault or harassment made.
The letter said Florida State initiated a Title IX investigation in November 2013, more than nine months after first learning about the incident, but the woman’s then-attorney told the school to "cease all contact with her client.” Campus police, who learned about the incident in December 2012, also didn't initiate a Title IX investigation.
The Department of Education's Office for Civil Rights is currently investigating about 70 other institutions on the way they handle sexual assault complaints.
- Scooby Axson