Chile last week asked the world football governing body to investigate allegations that right-back Byron Castillo is actually Colombian and not eligible to represent Ecuador.
Castillo played eight times for Ecuador in South American qualifying, including a goalless draw with Chile in September and a 2-0 victory in November.
La Roja finished seventh, meaning they just missed out on a play-off spot, but believe Ecuador should be expelled from the quadrennial competition.
And FIFA confirmed on Thursday that it is looking into the recent complaint made by the Federacion de Futbol de Chile.
The statement read: "FIFA has decided to open disciplinary proceedings in relation to Byron David Castillo Segura's possible breach of the call criteria for the indicated matches.
"In this context, the FEF and the Peruvian Football Federation have been invited to present their positions before the FIFA Disciplinary Committee."
Ecuador have already been drawn in Group A at the World Cup, alongside host Qatar, as well as Senegal and the Netherlands.
FIFA sanctioned Bolivia for fielding ineligible player Nelson Cabrera in 2018 World Cup qualifiers against Peru and Chile, awarding its opponent 3-0 wins in both instances.