A computer-implemented method for configuring application control rules in a network with existing application control rules, comprising: generating, by an administrative server located in the network, a new application control rule that specifies restrictions or a permission on executing a software application, a function of an application or a category of applications; collecting information about one or more computers in the network by the administrative server, the information comprising information about software applications deployed on the one or more computers and one or more existing application control rules associated with the software applications, wherein the information about a software application of the software applications includes at least one of a version of the software application, a unique identifier of the software application, a digital signature of the software application, data about a manufacturer of the software application, metadata of the software application, or a way in which the software application was installed; testing, by a processor of the administrative server, the new application control rule using the collected information to determine verdicts rendered by the new application control rule that restrict or permit an execution of the software application, the function of an application or the category of applications; comparing, by the administrative server, verdicts rendered by the new application control rule with the verdicts rendered by the existing application control rules to identify conflicts between the compared rules; and upon detecting a conflict between the compared rules, determining, by the administrative server, a priority between the new application control rule and the one or more existing application control rules, and depending on the determined priority of the rules, reconfiguring one of the compared rules to eliminate the conflict. generating, by an administrative server located in the network, a new application control rule that specifies restrictions or a permission on executing a software application, a function of an application or a category of applications; collecting information about one or more computers in the network by the administrative server, the information comprising information about software applications deployed on the one or more computers and one or more existing application control rules associated with the software applications, wherein the information about a software application of the software applications includes at least one of a version of the software application, a unique identifier of the software application, a digital signature of the software application, data about a manufacturer of the software application, metadata of the software application, or a way in which the software application was installed; testing, by a processor of the administrative server, the new application control rule using the collected information to determine verdicts rendered by the new application control rule that restrict or permit an execution of the software application, the function of an application or the category of applications; comparing, by the administrative server, verdicts rendered by the new application control rule with the verdicts rendered by the existing application control rules to identify conflicts between the compared rules; and upon detecting a conflict between the compared rules, determining, by the administrative server, a priority between the new application control rule and the one or more existing application control rules, and depending on the determined priority of the rules, reconfiguring one of the compared rules to eliminate the conflict.