"We will work aggressively with our members to amend our bylaws so that this type of behavior is not a part of intercollegiate athletics," Emmert said.
His comments came one day after the NCAA ruled that Newton would not lose his eligibility at Auburn despite evidence that Newton's father had attempted to obtain money from at least one university in exchange for the quarterback's services.
The NCAA announced Wednesday that Newton's father would be limited in his association with the Auburn athletic program.
Undefeated Auburn will play on Saturday in the Southeastern Conference championship game against South Carolina. A win in that contest would put Auburn in the national championship game.
The NCAA's investigation failed to reveal any proof Newton knew his father had, in effect, attempted to sell Newton to the highest bidder.
"We recognize that many people are outraged at the notion that a parent or anyone else could 'shop around' a student-athlete and there would possibly not be repercussions on the student-athlete's eligibility," Emmert said.
"I'm committed to further clarifying and strengthening our recruiting and amateurism rules so they promote appropriate behavior by students, parents, coaches and third parties."
Newton has thrown for 2,254 yards and 24 touchdowns this season and run for 1,336 additional yards and 18 scores.