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.