The game in Quito, which the hosts won 2-0, went ahead even though a torrential downpour had left large areas of the Atahualpa stadium pitch under water.
"It's farcical. The health and safety of players must prevail over all other considerations," said FIFPro spokesman Andrew Orsatti in an emailed statement to Reuters.
"This also raises concerns about the pressure to fulfil commitments stemming from what is a jam-packed calendar of matches," he added.
"Has this been adequately balanced between the needs of clubs, countries, and how to protect players in a manner that maximises their performance?"
Ecuador's squad, in particular, is made up largely of players based in Europe and Mexico, and they were expected to be back with their clubs in time for league matches this weekend.
"When players get together for a national team camp, all involved, from federations, fans, sponsors to broadcasters, may also have an expectation to get players on the pitch, no matter what the cost," added the statement.
"That is a situation we must avoid and FIFPro believes the match calendar must be constantly revised to eliminate the risks associated."
Ecuador coach Gustavo Quinteros said that the pitch was his team's "biggest opponent" during the match in Quito, which lies 2,800 metres above sea level.
A spokesperson for soccer's governing body, FIFA, said that under the laws of the game and World Cup regulations, the decision on whether to play lay "solely with the referee, who in this case deemed the pitch playable".
(Editing by Neville Dalton)
