Five top-flight games were due to be played on Wednesday, but with several clubs still owing salaries to players a strike was called.
The Ecuadorian Footballers' Association (AFE) also revealed Sunday's matches could be postponed if no resolution is found.
The union urged the Ecuadorian Football Federation (FEF) to do more to resolve the matter and talks are due to take place on Thursday in an attempt to avoid another strike.
AFE vice-president Edwin Tenorio told AFP: "As expected, the strike began on Wednesday and we are in talks to find a settlement.
"We hope to reach agreement as soon as possible and [one that is] satisfactory to all members."
Some clubs are reported to owe players wages that were due 11 months ago.