The presented previously indirect optimization method (IOM) developed within biochemical systems theory (BST) provides a versatile and mathematically tractable optimization strategy for biochemical systems. However, due to the local approximations nature of the BST formalism, the iterative version of this technique possibly does not yield the true optimum solution. In this work, an algorithm is proposed to obtain the correct and consistent optimum steady-state operating point of biochemical systems. The existing linear optimization problem of the direct IOM approach is modified by adding an equality constraint of describing the consistency of solutions between the S-system and the original model. Lagrangian analysis is employed to derive the first order necessary optimality conditions for the above modified optimization problem. This leads to a procedure that may be regarded as a modified iterative IOM approach in which the optimization objective function includes an extra linear term. The extra term contains a comparison of metabolite concentration derivatives with respect to the enzyme activities between the S-system and the original model and ensures that the new algorithm is still carried out within linear programming techniques. The presented framework is applied to several biochemical systems and shown to the tractability and effectiveness of the method. The simulation is also studied to investigate the convergence properties of the algorithm and to give a performance comparison of standard and modified iterative IOM approach. (C) 2007 Elsevier Ltd. All rights reserved.