Men's basketball was one of four Auburn sports that failed to meet Academic Progress Rate scores. Men's swimming and men's track were the other two sports that fell below the required rate.
At Alabama, men's basketball was the only program to fall under the benchmark.
At Auburn, the result of 899 score means a loss one of its 13 full scholarships. At Alabama, the score of 922 won't result in immediate penalties because no players failed to regain eligibility in the subsequent reporting period after being ruled ineligible.
In a statement released by the university, Auburn athletics director Jay Jacobs said the failure is "unacceptable."
"While we are pleased that 18 of our 21 sports met the NCAA's benchmark for academic progress," he said, "we will not be satisfied until all of our sports reach this level. Failure to meet the benchmarks set forth by the NCAA under its academic reform program is unacceptable. In this case, we decided to be aggressive in getting this behind us, so the penalties have already been taken for the current academic year."
Alabama didn't see its score as any type of trend that required attention.
"We're confident that the men's basketball decline is a one-year aberration and that we will post a much better score next year, although it should be noted that the actual score for that team was down only six points from last year's report," said Jon Dever, Alabama's assistant athletics director for student services.
The NCAA established the APR to monitor academic progress and retention among its universities. Programs are awarded for players that remain academically eligible and remain with the team.
The APR is based on a 1,000-point scale. Any score below 925 is subject to penalty, as the three Auburn teams were when they fell below the mark.
The other 18 sports teams, including football, finished above the 925 mark.
Only one SEC football team, Ole Miss, missed the cut. As a result, the Rebels will lose three scholarships.
In the state, UAB was the only Football Bowl Subdivision school to have practice times cut in both football and men's basketball because of subpar academic scores. New Mexico State was the only other FBS team that was an offender in both men's basketball and football.
UAB lost one scholarship in men's basketball but was spared a similar penalty in football because of a rise in scores last year that weren't counted in the latest score.
"The priority that I had when I came in to take this job as the UAB AD (in February 2007) was to instill an academic excellence culture," UAB athletic director Brian Mackin said. "I think we invested with people, with our academic staff and technology. Adding those two elements, we definitely changed the culture academically and the trend is up and headed in the right direction."