The 31-year-old forward was recalled last week for the African Nations Cup final round first leg against Cape Verde Islands on Sept. 8, eight months after he was suspended for having led a player strike over unpaid bonuses.
The row caused Cameroon to cancel a friendly in Algeria.
"I regret to inform you I've decided not to participate in any game with the national team since the flaws I kept denouncing as a captain have not been solved," Eto'o wrote in a letter to the Cameroon soccer federation published on his website.
"The national team environment is still made up of amateurism and bad management which do not suit the requirements for high-level sport," added the four-times African Footballer of the Year who has played for his country more than 100 times.
"I am sure all (Indomitable) Lions lovers will understand my move which is only aimed at drawing attention on the necessity to have a more professional management of this team," added former Inter Milan and Barcelona player Eto'o.
"This team is an institution which brought a lot to our country and we can still expect a lot from it."
Eto'o now plays for wealthy Russian Premier League side Anzhi Makhachkala.
The two-legged match between Cameroon and Cape Verde Islands will decide a place at the 2013 finals in South Africa.
The return leg is in Yaounde in October.