Schlissel, who is in his first year as president, singled out the football team's low graduation rate during a faculty meeting on Monday.
"These past two years have gotten better, but before that, the graduation rates were terrible, with football somewhere in the 50s and 60s when our total six-year rate at the university is somewhere near 90%. So that's a challenge."
On Tuesday, he apologized to Hoke and interim athletic director James Hackett.
"I have a great deal of respect for the efforts of our student-athletes and for the coaches and others in athletics who support them, and that did not come through in my earlier comments," Schlissel said in a question and answer with university spokesman Rick Fitzgerald, published on the university's web site early Wednesday morning. "I regret that."
Athletic director Dave Brandon resigned last month, and Schlissel has said that he is not going to rush the process of hiring a new permanent athletic director. Schlissel, who was previously the provost at Brown, said he wants to hire someone with a similar view on the relationship between athletics and academics.
In his comments on Tuesday, Schlissel said he was happy with Michigan's athletic department, which has an 88 percent graduation rate. The Free Press reports the football team's graduation rate is 69 percent for students who entered during the 2007-2008 academic year.
Michigan has won its last two games and is 5-5 on the season. The Wolverines are idle this week before hosting Maryland on Nov. 22 and closing the regular season on the road against Ohio State on Nov. 29.
- Paul Palladino