Mexican fans were were heard directing abuse at Poland striker Robert Lewandowski after he saw his second-half penalty saved by goalkeeper Guillermo Ochoa during Tuesday's 0-0 draw with Poland.
In a statement confirming the proceedings on Wednesday, FIFA did not elaborate on the nature of the chants.
“The FIFA Disciplinary Committee has opened proceedings against the Mexican Football Association due to chants by Mexican supporters during the Mexico v Poland FIFA World Cup match played on 22 November,” it said.
“The proceedings were opened on the basis of article 13 of the FIFA Disciplinary Code.”
The Mexican federation received 12 sanctions during qualification for the 2018 World Cup leading to two home games being played behind closed doors.
FIFA had also opened disciplinary proceedings against Ecuador after allegations against their fans in their World Cup opener against Qatar on Sunday.
Additional reporting by Reuters.