The penalties, announced Tuesday by the NCAA's Division I Committee on Infractions, include scholarship reductions in football, men's and women's basketball, baseball, men's and women's track and field, men's golf, softball, women's soccer and volleyball.
The athletic department will be on probation for four years, has been fined $25,000, must submit to an external audit of its compliance system and will vacate victories and records from the 2005-06 academic year through 2009-10.
The ruling comes as the Lions' football team prepares to host a quarterfinal FCS playoff game against New Hampshire on Saturday. Their playoff run will not be affected by the NCAA's decision, which did not call for any postseason bans.
The infractions were reported to the NCAA by Southeastern Louisiana, which proposed sanctions and voluntarily began serving them during this academic year.
The NCAA accepted Southeastern's proposed scholarship reductions.
"We are pleased to put resolution of this case behind us," athletic director Jay Artigues said in a statement. "These infractions occurred years ago, and current coaches, staff and administration are absolutely committed to ongoing compliance with all NCAA rules."
The scholarship reductions include:
— Football from 63 to 60 in the 2013 and 2014 seasons, and to 62 in 2015.
— Men's basketball from 13 to 11 this season and to 12 for the following two seasons.
— Baseball from 11.7 to 10.7 for the 2014 and 2015 seasons.
— Women's basketball from 15 to 14 for this and next season.
Southeastern's report to the NCAA, obtained through a freedom of information act request by The Associated Press in April, indicated that most violations occurred in football and men's basketball.
During the 2007 football season, Southeastern allowed 18 players to compete while ineligible, and 17 the season before. The men's basketball team had a high of seven ineligible players during its 2006-07 season.
While Southeastern stressed there was no evidence that an athlete was deliberately certified improperly, the university acknowledged a lack of institutional control and said it "should have known the students did not meet NCAA requirements based on academic and other records available at the time."
The report asserted that certain former compliance officials' misunderstanding of NCAA rules, turnover in the athletic department and records that went missing, possibly when they were moved during a renovation, all contributed to compliance problems. The report specifically cited former compliance coordinator Greg Harrod's "apparent misunderstanding" of NCAA rules while he worked at Southeastern from 2000-06.
It also stated that the compliance staff was not increased when football was brought back to Southeastern in 2003, adding about 125 athletes.
The report said in 90 percent of the cases, ineligibility resulted from the timing of a degree change, and that 86 percent of all ineligible athletes wound up graduating. Most would have remained eligible had they been properly advised about NCAA deadlines for changing majors, the report stated.