The incident in the Liga MX contest at Estadio Corregidora occurred midway in the second half that saw supporters spill onto the pitch.
Initially, local reports in Mexico said that up to 17 people had been killed, while other reports suggest two have died.
However, officials from the Coordination of Civil Protection of the State of Querétaro stated that 22 people were taken to hospital, with two in critical condition.
Officials in Mexico have said a full investigation will take place.
"The Mexican Football Federation regrets and condemns the events that occurred this afternoon at Estadio Corregidora in Queretaro, in the match between Queretaro and Atlas," read a Mexican Football Federation statement.
"Football must be a space of healthy coexistence where any type of violence is inadmissible.
"The FMF will monitor and assist in the investigation process with the corresponding instances so that those responsible are sanctioned in an exemplary manner."
Liga MX president Mikel Arriola insisted any breakdown in stadium security would be investigated swiftly.
"Those responsible for the lack of security in the stadium will be punished in an exemplary manner," Arriola said on Twitter.
"The safety of our players and fans is a priority."
Queretaro have also stated they will aid with all investigations.
"We roundly condemn the events that occurred at Estadio Corregidora," read a club statement.
"We are in full communication and coordination with the authorities so that they can act quickly against anyone responsible.
"As an institution we condemn violence of any kind."
Atlas echoed those words, insisting football must be able to promote family values.
"Atlas FC regrets and disapproves of the events that took place in Estadio Corregidora," their statement read.
"Soccer must be an ally to promote values and fun for the whole family.
"We request the pertinent authorities, the Liga BBVA MX and the FMF, to investigate thoroughly and reach the ultimate consequences, determining the responsibilities of those who are involved, and applying the full force of the law."