The dataset indicates the problem factors which may influence the development of partnering relationship between two key project parties - the main contractor and the subcontractor. A total of 53 problem factors were identified and were clustered into five categories. An online questionnaire was used to elicit the viewpoints of these key parties with regards to the extent to which the factors have an impact on the partnering relationship in the Malaysian construction industry. The target respondents were managers and engineers of various construction companies in Malaysia with the main contractors or subcontractors who have projects in Kuala Lumpur, Shanghai and New Delhi. Both descriptive and quantitative analysis approaches were used to present the data. Relative Importance Index method was used to determine the top challenges to building favourable partnering relationships; and Partial Least Squares Structural-Equation Modelling (PLS-SEM) analysis was conducted to examine the role played by each cluster of factors in explaining the quality of partnering relationship between the main contractors and subcontractors. This data set would assist practitioners to work on the major problem factors to improve the quality of partnering relationship between the key participants in their present and future construction projects. By eliminating or minimizing these problem factors, practitioners will contribute significantly to effective supply chain management in the construction industry. The data would be of value to academics and industry professionals involved in the construction business domestically and internationally.