According to reports, discriminatory chants were allegedly sung by the country's fans at the tournament's opening game against Qatar.
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The alleged chants at the Al Bayt Stadium are said to have been about Chile, who brought a legal case ahead of the competition as they tried to take Ecuador's place.
Chile accused Ecuador of using an ineligible player, but ultimately lost the legal battle to fight for their place at Qatar.
As a result of the chants, FIFA have cited the section of its disciplinary code dealing with discrimination to the Ecuadorian soccer federation.
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No timetable has been given for the punishment, though.
Ecuador's fans also made headlines after chanting about there not being any alcohol at this year's World Cup.
The South Americans sung 'we want beer' whilst their side sealed a 2-0 win over the hosts.
Gustavo Alfaro's side next face joint-Group A leaders the Netherlands on Friday at 4pm.