Charges filed against the demonstrators range from trespassing to "wearing a mask," a violation of a rarely invoked 1951 law originally aimed at fighting the Ku Klux Klan.
Those arrested were among about a record 16,000 people who demonstrated outside the Western Hemisphere Institute for Security Cooperation at Fort Benning, calling for the school to be shut down.
Organizers of the protest said concern about the war in Iraq and President Bush's re-election boosted attendance at this year's event.
Oscar-winning actress Susan Sarandon addressed the group Saturday, and Martin Sheen, who plays the president in NBC's "West Wing" TV series, delivered a fiery speech Sunday.
"We gather to revive the memory of those who have died at the hands of this combat school," said the Rev. Roy Bourgeois, a Catholic priest. "How do you teach democracy behind the barrel of a gun? If they are so concerned about teaching democracy, then why not close this school and send these students to some of our fine universities."
Bourgeois is head of SOA Watch, which monitors the institution formerly known as The School of the Americas. The group has staged annual protests there since 1990.
SOA Watch and other critics allege the school's graduates have committed murder, rape and torture, including the murders of six Jesuit priests, their housekeeper and her daughter in El Salvador in 1989.
Seventeen of the arrests Sunday came after some protesters scaled chain-link fences onto military property, said Bill Quigley, legal adviser for the protest group.
The school trains soldiers, police and government officials. SOA Watch claims some of its graduates were involved in a string of human rights abuses in the 1980s and even now exploit the people and resources of Latin America.
As recently as October, a former Colombian army officer who graduated from the school had been accused of murdering a state official while still a member of the military. Maj. David Hernandez, who became the head of a paramilitary group, was killed in a clash with army troops.
Defense officials have steadfastly disputed the group's claims about the school. In the past, Army officials have held news conferences to deny allegations, but days before Sunday's event the Army said it would have no comment.