Cost estimation is particularly difficult, often leading to considerable deviations. For capital projects, especially transport infrastructure projects, deviations hover around an average of 28% of the estimated cost. There are several factors that cause these deviations between the final accounts and the contract sum. How these factors combine to cause deviations between the contract sum and the final account in recent times has been of great concern to construction managers and researchers alike. This study sought to identify the significant factors that result in deviations between contract sums and the final accounts of capital projects. Using a sample size of 45, comprising contractors, consultants, and clients, the factors identified using Relative Important Indices were “price fluctuations,” “late material delivery,” “changes in the scope of work,” “fluctuations in the market demand,” and “changes in design.” Using Kendall’s coefficient of concordance, a coefficient p value of 0.068 was obtained. As such, the null hypothesis was rejected as there was a level of agreement among the respondents. Again, based on a significance test run, 26 out of the 40 identified factors used for the analysis were seen to be significant in influencing the deviations between contract sums and final accounts figures.