The Ecuadorian Football Federation are to protest to FIFA over Wigan midfielder Luis Antonio Valencia's absence from last week's international friendly against Colombia.
PSV Eindhoven midfielder Edison Mendez has been left out of the Ecuador squad to face Argentina on Sunday after failing to recover from injury.
Brazil's Pele has criticised FIFA's recent decision to lift a ban on playing World Cup qualifiers at more than 2,750 metres above sea level.
Midfielder Edison Mendez has been included in Ecuador's squad for World Cup qualifiers against Argentina and Colombia after going back on his decision to quit the national side.
Ecuador included English-based pair Antonio Valencia and Felipe Caicedo in their 24-man squad on Thursday for this month's home friendly with Haiti in the provincial town of Latacunga on March 26.
Ecuador coach Luis Fernando Suarez resigned immediately after his side were thrashed 5-1 by Paraguay. The defeat left them bottom of the South American group with no points.
Ecuador have left captain Ivan Hurtado and right back Ulises de la Cruz out of their squad for this month's World Cup qualifiers against Paraguay and Peru.
Goalkeeper Marcelo Elizaga became Ecuador's latest injury worry on Tuesday when he suffered a cut on his head during a training match.
Defender Ulises de la Cruz and striker Ivan Kaviedes have been recalled by Ecuador for World Cup qualifiers against Venezuela and Brazil this month.
Striker Cristian Benitez scored twice to help Ecuador to a crushing 5-1 win over nine-man El Salvador. The visitors were beaten by the same score on their previous visit to South America.