The Blues forward, who will leave the club this summer, was part of the 23-man squad who refused to board the plane to Brazil in a dispute over bonus payments last week.
The players were reportedly unhappy that their payments were less than had been previously agreed, with striker and talisman Eto'o leading the disgruntled voices.
The Indomitable Lions eventually departed for Brazil with coach Volker Finke telling Sport1: "It's just one of those things that these agreements can take longer in Africa. That agreement was struck this morning and now we can fly to Brazil today.
"Our fans will be pleased, Cameroon will of course be participating in the World Cup."
Cameroon football president Joseph Owna said: "Everything has been resolved. We have opted for transparency. There is no problem and the team needs to all look in one direction."
A report by The Independent has claimed that Cameroon daily newspaper, Mutations, has been hugely critical of the legendary Cameroon striker.
It wrote “We must now ask: which country do Eto’o and his comrades represent if they go to Brazil having refused to accept this country’s most precious symbol, its flag?
“The flag is a symbol of the nation. We can blame those in power [for our problems], but insulting the national anthem or trampling the flag is a sacrilege.
“That is the great sin of the ‘Indomitable Lions’, when they rushed as one man into the locker room and refused to receive the flag from the prime minister.
“A player who goes to the World Cup is a soldier at the front. If he does not want to board that is high treason that deserves punishment.”
The African nation kick off their campaign against Mexico in Group A on Friday evening, following Brazil's 3-1 win against Croatia in the same group on Thursday night.
Eto'o will leave Chelsea this summer after nine goals in 21 appearances for the Blues.