Amnesty International is asking the Mexican government to examine claims that state officials used torture and abductions during protests in the city of Oaxaca last year.
Irene Khan, Amnesty International secretary general, called for the investigation during a visit to Oaxaca on Tuesday.
She has said that Ulises Ruiz, governor of Oaxaca, is implicated in the abuses.
After meeting with Khan, Ruiz has said that Amnesty is wrong and that the human rights organisation had not asked his government for its side of the story.
Ruiz said: "She's not well informed ... the information is biased.
"We let them know that the authors of Amnesty International's report are even advisers to [the protesters]."
The political upheaval began last year as a strike by teachers demanding higher pay.
A broader movement was then created, known as the People's Assembly of Oaxaca (APPO).
It included indigenous groups, students, farmers and left-wing activists who accuse Ruiz of rigging his electoral victory.
The strikes resulted in a confrontation with police that lasted for months.
More than 20 people were killed and protesters have said that more than a dozen of the dead were activists killed by police.
Amnesty has said that state officials may have tortured protestors that were arrested, and committed other human rights abuses that should be investigated by outside authorities.
Khan said: "For the governor not to read our report seriously ... is simply an excuse."
"Amnesty International's reputation stands on itself."
Meanwhile, riots in July resulted in protesters burning buses and fighting police during an indigenous cultural festival.