The civil engineering project, by its very nature, is a big user of natural resources. Nevertheless, with growing concerns on the climate change and the limit nature of these resources, there is increasing pressure to ensure the implementation of the construction to be completed within the stipulated quality, cost and time. This is due to the severity impacts on the environment it causes in the event that there is prolongation in the construction duration or face abandonment. Hence, this study looks upon the occurrence of unauthorised instructions as it is among the significant factor causing the project problems and delay. This paper aims to investigate the occurrence of unauthorised instruction in civil engineering projects and to determine the significant factors causing it. The data was obtained from professional civil engineers and Grade G7 contractors registered with their respective organisations i.e Board of Engineers Malaysia (BEM) and the Construction Industry Development Board (CIDB). From 288 questionnaire survey returns, this study determined that the occurrence of unauthorised instructions in civil engineering projects in Malaysia was at a moderate level. There were seven significant factors contributing to it namely poor in complying with the condition of contract, level of understanding condition of contract, ground uncertainty, the familiarity of procurement method used, tight project milestone, clarity of SFoC and project complexity. These seven factors if properly understood and be put more concern by all parties at the onset of every project may ensure the project can be successfully completed on time and eventually could reduce damage to the environment.