Wigan are to be reported to Fifa by the Ecuadorian Football Federation over Antonio Valencia's no-show for their friendly against Colombia last week.
Reports in Ecuador suggested that Valencia missed the game in America because of a knee injury but he then played for the Latics in their 1-0 defeat by Chelsea on Sunday.
EFF president Luis Chiriboga Acosta told reporters: "We are sending a formal complaint to FIFA.
"Neither the club nor him have a justification for this absence. The only thing we can see is that Valencia does not want to represent the Ecuadorian national team.
"If he didn't join the team because he is scared of being excluded from the Wigan starting line-up, it's unacceptable.
"Valencia should have joined the national team without making excuses. He was the one who decided not to play against Colombia."
Ecuador coach Sixto Vizuete has now left Valencia out of his squad for two World Cup qualifiers next month, although the midfielder was already banned for one game.
However, he said that the door had been left open to Valencia for "when the real reason for his absence is clarified."