Eto'o has been in Qatar as head of the delegation from Cameroon, which was eliminated in the group stage last week.
"I have been the target of insults and allegations of cheating without any evidence," he wrote Tuesday. "I pledge to continue to resist the relentless provocation and daily harassment of some Algerian supporters."
Eto'o is part of the FIFA Legends program that uses former players to promote soccer and it was unclear in what capacity Eto'o attended the game Monday night.
Qatari organizers of the World Cup said Eto'o hadn't been their guest at the game.
FIFA didn't immediately respond to a request for comment. A spokesman for the Cameroon federation didn't immediately answer phone calls or respond to messages seeking comment.
Qatar's government did not immediately respond to questions about the incident.
Eto'o played at four World Cups for Cameroon between 1998 and 2014, and was elected to lead its soccer federation one year ago.
He called on Algerian soccer officials "to put an end to this unhealthy climate before a more serious tragedy occurs."
"To Fennecs' fans," he said, noting the Algeria team's nickname, "I wish that they find peace and manage to overcome the disappointment of a painful defeat, now behind us."