Abstract: The subject of the research is economic and mathematical tools of optimization of financing of innovative projects implemente by military industrial enterprises. A formalized statement of the problem of the adjustment of the current funding available for the implementation of innovative projects in conditions of irregular funding is proposed. The method of solving this problem, which is based on the optimization model smoothing the coherence profile to the actual distributions in the previous funding round is developed. As for the first phase of funding for the retrospective distribution profiles are not available, in addition an optimization formulation of the problem of distribution of current appropriation without regard to historical distribution profiles is proposed. The problem of selection of objective function in optimization model is reviewed. The principle of compromise based on the principle of equitable assignment, solves the problem of multicriteria radical way due to the convolution of the set of criteria into one integrated criterion. The scientific novelty is caused by the development of a new methodology for adjustment of management decisions, aimed at financing innovative projects in the military-industrial complex. The problem solution is considered for four types of target functions, respectively, a predetermined additive, multiplicative, and quasidisjunctive and quasiconjunctive operators of aggregation. The practical use of the developed models and algorithms is reviewed in a number of examples.