Amnesty International interviewed women who said they were abused after their arrests during disturbances in San Salvador Atenco.
The group has called for federal justice officials to take over the investigation, saying state authorities have ignored the claims and, in some cases, covered up evidence.
"These crimes are acts of torture under international law and the authorities must ensure that those responsible are held to account," said Kerrie Howard, deputy directory of Amnesty's Americas programme.
"It is high time for the federal prosecutor on crimes against women to take over."
The women were arrested after a police attempt to evict flower sellers erupted in violence, with hundreds of protesters fighting police.
Two protesters were killed and several police were beaten or taken hostage.
"When I arrived at the prison, the forensic doctor did not want to certify that I had been raped, it seems unfair to me that I shouldn't be believed"
Alleged victim, Amnesty report
The worst violence happened when police stormed the town the next day, Amnesty said. Police arrested more than 200 people, severely beating many of them.
The women allege they were punched and kicked while being transported to prison.
Some said they were raped or forced into other sex acts with agents.
"When I arrived at the prison, the forensic doctor did not want to certify that I had been raped," one victim told Amnesty.
"It seems unfair to me that I shouldn't be believed."
Enrique Pena, the state governor, has said the abuse claims were a tactic by "subversive groups" to discredit his government, and said investigations could not take place until official complaints were filed.
However, Amnesty said the state government first prevented the women from giving evidence - either through intimidation or by refusing to record what happened - and has since failed to investigate the complaints.
Vicente Fox, president of Mexico, had pledged to clean up Mexico's poor rights record after his rise to power in 2000 ended 71 years of one-party rule.
However, Howard said in Amnesty's reporty that the case was Fox's "last chance" to show a commitment to ending violence against women and fulfilling its human rights obligations.