Emmert's statements came a day after the NCAA reinstated the Auburn quarterback's eligibility in time for the SEC championship game.
Newton was briefly ruled ineligible Tuesday for violations the NCAA concluded his father, Cecil, committed during the quarterback's recruitment last fall.
The NCAA said Newton didn't know his father engaged in pay-for-play talks with Mississippi State. Auburn applied for Newton's reinstatement immediately, and his eligibility was restored Wednesday with no conditions.
Criticism came swiftly after the ruling went public, prompting Emmert to make clarifying statements.
"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," he wrote.
"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."
But he noted many in the media and public have wrongly compared the Newton ruling to other high-profile NCAA cases while ignoring the differences.
"While comparisons may be human nature," he wrote, "they should at least be made based on the facts."
Emmert wrote the NCAA makes each decision based on its merits, adding that no two are identical.
"In the Cam Newton reinstatement case, there was not sufficient evidence available to establish he had any knowledge of his father’s actions and there was no indication he actually received any impermissible benefit," he wrote.
"If a student-athlete does not receive tangible benefits, that is a different situation from a student-athlete or family member who receives cash, housing or other benefits or knowingly competes and is compensated as a professional athlete."
Emmert also made clear the distinction between how the NCAA determines the university's culpability and the student-athlete's.
"Universities are accountable for rules violations through the infractions process," he wrote. "Student-athletes are responsible for rules violations through the eligibility process."
He reiterated that the reinstatement process is likely to conclude before the close of an investigation. The NCAA said Wednesday that the Newton case is not officially closed.
Many have questioned the decision's timing, considering SEC championship game takes place Saturday, when Auburn will try to clinch a spot in the BCS national championship game.
Emmert wrote that the NCAA tries to be as timely and thorough as possible.
"Sometimes decisions are rendered in one day and other times it takes longer given the complexity of the matter," he wrote. "In all cases, the staff is aware of the next date of competition for the student and does everything possible to render a decision before that date."
The Newton family lawyer, George Lawson, also spoke for the first time since the ruling, telling Atlanta TV reporter Mark Winne that the Newtons never accepted money for their son's services.
He said Cam is "relieved" and "confident" now that his eligibility has been clarified by the NCAA.
“I would hope that it would be at an end," Lawson said of the ordeal. "But if it is not at an end, Cam and his family will continue to participate.”