The Chelsea forward missed two days of training due to a knee complaint, which has been troubling him since the end of the Premier League season.
As a result, Cameroon's all-time top goalscorer will be unable to help his nation as they bid to pick up their first points of the campaign.
Eto'o wrote on Twitter: "The doctors confirm! I would probably not be able to play the match vs Croatia on Wed June 18th due to an injury on my knee causing me pain."
Cameroon suffered a 1-0 defeat to Mexico in their opening match of the tournament last week.