Emmert, in an internal letter obtained by CBSSports.com, said it was "inaccurate" to say that no cases have been handled by the infractions committee in the last year.
Last week, Big 12 Commissioner Bob Bowlsby said that "cheating pays" in the NCAA because the organization wasn't minding the store as it fights off criticism and lawsuits.
Emmert's letter, delivered to all 32 Division 1 conference leaders, did not mention Bowlsby by name but did state that the NCAA was currently working on 100 enforcement cases.
The NCAA has been in damage control mode for months while dealing with criticism and court cases.
The NCAA on Tuesday settled a class-action concussion lawsuit brought by former college athletes. The reported settlement is $70 million.