FECAFOOT said players could be punished through the internal investigation ahead of Cameroon's final Group A game against Brazil on Monday.
Cameroon is already eliminated after two poor performances in losses to Mexico and Croatia.
Toward the end of the game against the Croatians in Manaus on Wednesday, Assou-Ekotto thrust his head into the face of Benjamin Moukandjo and the pair scuffled in front of their goal before being separated by another Cameroon player.
"The recent acts of violence that took place during the match against Croatia do not reflect the values of fair play and respect as promoted by our federation," FECAFOOT said. The "disgraceful behavior is being further investigated internally."
After the game, Cameroon's German coach, Volker Finke, said the scuffle between Assou-Ekotto and Moukandjo was "unimaginable" and that he would find out "why exactly these two players exploded" on the pitch.
"I think that this team has shown some things that are not acceptable and there will be consequences for the players involved, definitely," Finke said.
The players initially refused to board a plane for Brazil over a dispute with the federation over bonuses. They then produced two insipid performances to be eliminated without scoring a goal.
The West Africans finish against Brazil in Brasilia, when they again face leaving a World Cup after losing all three games. Cameroon lost all its games in South Africa four years ago.
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