The article is exposed the approach to the development of the program of organizational and functional transformations taking into account the features of the developed (improved) process of interorganization co -operation. Types of interdependence of business-operations of process interorganization collaboration are defined. The recommendations for transformation of scheme of responsibility and accountability, improving the communication process, system of motivation, methods of co-ordination and control of realization of strategy of interorganization co-operation are emphasized.