The N.C.A.A. on Tuesday cited Miami for a decade of violations in its men’s basketball and football programs, penalizing the university with three years of probation and a loss of some scholarships.

A 102-page infractions report by the N.C.A.A. concluded that Miami “lacked institutional control” over the programs as it failed to monitor a major booster, coaches and student-athletes. The penalties issued by the N.C.A.A. were in addition to the self-imposed penalties by Miami in recent years, which included a ban on bowl games in 2011 and 2012.

The N.C.A.A.’s punishment, which was accepted by Miami, ends its lengthy, high-profile investigation into the university’s athletics department. The football team, currently 6-0 and ranked seventh in the nation, will lose nine scholarships over three years, and the men’s basketball team will lose a scholarship in each of the next three seasons.

The inquiry, which dates to 2009, centered on allegations that a booster, Nevin Shapiro, gave hundreds of thousands of dollars in cash, as well as other benefits, to Miami athletes.