The resignations announced Monday include chairman Paul Parilla, vice chairman Jay Binder and treasurer Bitsy Kelley.
Former Team USA doctor Larry Nassar was jailed last year for 60 years for possessing child sex abuse images on his computer.
Three members of the USA Gymnastics Board of Directors resigned Monday.
Miller said Monday that she'll continue to fight the university over the billing - and over accusations that Michigan State heard complaints about Nassar sexually abusing patients for years, but did not act to stop him, NBC reports.
Some victims, including Olympic gymnast Aly Raisman, called out USA Gymnastics leadership for its actions throughout the case.
"Over the weekend, the USOC released a statement shamelessly taking credit for a few USA Gymnastics resignations (note: not fired), as though they are addressing this problem".More news: Netflix receives 8 Oscar nominations for 'Mudbound' and documentaries
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NCAA spokeswoman Stacey Osburn said Tuesday the organization has sent a letter of inquiry to the school "regarding potential NCAA rules violations related to the assaults Larry Nassar perpetrated against girls and young women, including some student-athletes at Michigan State". Perry previously called the women speaking out against Larry Nassar "courageous" in a statement.
In November, Nassar pled guilty to 10 counts of first-degree criminal sexual conduct.
Raisman questioned why USA Gymnastics president Perry did not stay for the entirety of the victim impact statements, and asked, "USA Gymnastics, where is the honesty?"
On the USA Gymnastics site, the newly vacant board positions are labeled "TBD", while the other member names remain.
Larry Nassar, the former team doctor of USA Gymnastics - who has been accused by hundreds of athletes of committing sexual abuse under the auspices of medical care - has been expunged from YouTube. In addition to his decades in prison for child pornography, he faces a minimum of 25 to 40 years for the assaults, according to the AP, though the maximum sentence could be significantly higher.
We're now hearing the sentencing could go the rest of this week, with 30 more victims expected to make statements.