In Building Information Modelling (BIM) based construction projects, several challenges persist in identifying the primary factors affecting disputes among collaborating entities. Thus, it is necessary to comprehend the distinctions in disputes among diverse types of organizations engaged. Therefore, this study aims to examine the relationship between critical factors affecting dispute negotiation in construction subcontracting in BIM-based construction projects. To achieve that aim, the objectives are to identify factors affecting dispute negotiation in subcontracting in BIM-based construction projects, determine the critical factors among different types of organizations involved, and create a model relationship between critical factors affecting dispute negotiation in construction subcontracting in BIM-based construction projects. A systematic literature review was carried out to generate a list of factors. Then, questionnaire survey data were collected among construction industry professionals. Data were analyzed using the normalized mean ranking method, Kruskal–Wallis H test, overlap analysis, and correlation analysis. The findings revealed ten critical factors affecting dispute negotiation in construction subcontracting for BIM-based construction projects include the following contract elements: clearly defined rights and responsibilities of both parties, strict penalty provisions, a well-defined scope of work, detailed procedures for dispute resolution, comprehensive management procedures, monitoring and control provisions, specified technical specifications for the project, insurance and guarantee provisions, clear risk allocation, and provisions for handling variations and adjustments. This is the first paper that analyses the relationship between critical factors in construction subcontracting in BIM-based construction projects. The study’s outcomes will furnish decision-makers with new evidence to reinforce BIM guidelines. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.