The construction sector is a key component of a nation's gross domestic product, but its inherent nature results in potentially dangerous conditions that affect the safety of all workers on construction projects (CPs). Therefore, the original idea of the research is to determine the relationship between safety system (SS) during the implementation phase (IPh) of CPs and the minimisation of waste (materials, time and cost). Achieving a lean construction work requires suitable planning, safety considerations and waste resource minimisation throughout the project cycle. This research aims to identify and rank the safety factors during the IPh of a CP, which will have positive effects on minimising waste. Information and data were gathered from the existing literature and the structured interviews and questionnaire survey conducted among 111 randomly selected construction companies. Questionnaire results were evaluated using statistical tools, such as hypothesis testing, analysis of variance and linear regression. This research identified and ranked 24 important safety factors with positive effects on minimising waste in CPs during IPh. The seven most important safety factors that should be considered to minimise material, time and cost wastage are as follows: handling, management, external factors, workers, procurement, site condition and appropriate scaffolding for SS. The best linear model was developed on the basis of the importance index of the identified factors. This model can predict the minimisation of waste (materials, time and cost) in CPs by using SS. Thus, the safety criteria and SS should be used during IPh to minimise waste on the basis of the developed model.