Yale officials acknowledged their failure in 2004 as the department began its investigation, the New Haven Register reported. The investigation was triggered by an article in the alumni magazine titled "Lux Veritas and Sexual Trespass," a play on Yale's motto "Lux et Veritas" or "Light and Truth."
"The correction of violations does not diminish the seriousness of not correctly reporting these incidents at the time they occurred," Mary Gust, head of the department's division of student aid and program compliance, said in an April letter to the university.
In addition to failing to report four sexual assaults in 2001 and 2002, Yale did not properly define its campus, federal officials said. The university should have included space at the Yale-New Haven Hospital used by teachers and students from its medical school.
A Yale spokesman said in an emailed statement that the university believes the fine is excessive, given the time that has passed.