Lou Anna K. Simon, the former president of Michigan State University, was charged on Tuesday with two felonies, accused of lying to the police about her knowledge of sexual abuse committed by Dr. Lawrence G. Nassar.

The charges were the latest blow against Michigan State, which employed Dr. Nassar for years as he preyed on young women, and a warning to other institutions about the consequences they could face for failing to stop abuse. As the scope of Dr. Nassar’s crimes has become clear, Michigan State leaders have been accused of ignoring warning signs, disrespecting victims, and covering up misconduct, and the university has been rocked by resignations, protests and a $500 million settlement.

John Manly, a lawyer for more than 100 women who were abused by Dr. Nassar, said the charges against the university’s highest-ranking official had brought his clients “a level of vindication that’s hard to describe.” Mr. Manly said the prosecution sent a signal to leaders of other organizations where abuse has taken place. “I think I’d be looking over my shoulder if I were them,” he said. “And if you really want to stop this sort of abuse, you’ve got to send people the message that, ‘You’re going to go to jail.’”

Dr. Simon, who resigned in January under pressure, was accused in court documents of falsely telling investigators that she did not know the nature of a Title IX complaint against Dr. Nassar in 2014.