Recently, contractor claims and the resulting disputes have become inherent features of municipal construction projects, consuming much of the financial resources of these public non-governmental institutions and causing harmful consequences. Although claims cannot be completely eliminated in any project, identifying their root causes can largely prevent their occurrence. This study investigates the causes of such claims. The effective factors were identified and presented to experts via a questionnaire. In the first step, statistical tests measured the probability of occurrence and the average probability of turning into disputes. In the second step, exploratory factor analysis (EFA) classified the dispute-causing factors and examined the probability of each group turning into a dispute. In the third step, the effective factors were ranked using the analytic hierarchy process (AHP). The findings showed that weak laws and lack of local regulations, failure to draft contracts tailored to the project, failure to anticipate issues in contract conditions, and payment delays most significantly contribute to disputes. Factor analysis revealed five main factors: weaknesses in laws and regulations, political-environmental factors, employer weaknesses, consultant weaknesses, and contractor weaknesses. AHP ranking indicated that employer and consultant weaknesses, along with weaknesses in laws and regulations—which underlie other weaknesses—have the greatest impact on disputes. The results highlight the need to develop local regulations, improve municipal contract structures, and establish a specialized institution for these matters.