This paper presents issues related to organisational problems for discrete manufacturing in a manufacturing company. A search of the issue under analysis allowed for the definition of the paper’s objective, thesis and establishment of research gaps. The aim of the publication is to show the issues related to manufacturing system organisation, selection of the optimal production scenario for discrete and unit manufacturing conditions with the company's limited internal and external determinants and to provide the application possibilities of the available software, enabling the correct organisation of manufacturing tasks in real time. A thesis was adopted in which decision-making capacity for organisational change was practically demonstrated with limited information on manufacturing resources. The small number of publications on the practical use of specialised organisational software supported by components of distributed intelligence in manufacturing companies under the Industry 5.0 concept was identified as a research gap. This paper is the result of the authors’ broader research work related to decision-making systems using distributed intelligence and the resulting necessary automatic organisational changes in discrete manufacturing systems. The paper is divided into two sections: the theoretical section and the testing section. The first section concisely presents the key issues of the problem under analysis, while the testing section frames the problem as a useful example that demonstrates the practical use of the methods presented.