Presidency members Nebojsa Radmanovic and Zeljko Komsic endorsed the budget at an extraordinary session in Sarajevo.
The adoption of the budget without Izetbegovic's consent is expected to further complicate relations in the six-party ruling coalition.
The Presidency concluded that there will be no salary cuts for those employed in state institutions or new hirings this year.
The Council of Ministers proposed the 2012 budget in the amount of 950 million convertible marks, but Izetbegovic's Party of Democratic Action (SDA) believes the amount is not enough to pay for the functioning of some key state institutions, including state-level police agencies.