Land disputes are among the primary issues that Land Administration Systems attempt to accommodate. They derive from a variety of purposes including law, history, culture, traditions, administration and local geographical characteristics. There is no uniform approach in addressing land disputes and each country implements different resolution techniques. Ecclesiastical and monastic institutions throughout the world are owners of immense real estate property to such an extent that can indeed affect land administration policies. Greece is in the limelight of international attention due to its economical crisis and actually under pressure to modernise its dysfunctional land policy framework and create a stable investment environment. Within this framework, this paper investigates issues hindering proper land administration in Greece through the examination of a the resolving process regarding a case study in the island of Crete; a complex legal land dispute between the Greek State, two ecclesiastical institutions, a monastery and a church, and squatters took place, lasting for nearly 40 years. In order to evaluate this procedure and its impact on the development of the disputed area, a variety of data sources were accumulated and processed through time-based analysis. In this direction, cadastral survey’s contribution was examined along with land use change analysis, indicating how uncertainties in securing property rights on land, result in illegalities and trespassing posing significant barriers in land administration and management in the course of time. Although old and ambiguous in describing land boundaries the monasterial documentation might be, it proved sufficient to prevail over other litigants claims; the monastery was even adjudicated more than twice the size of the area that was claiming. By this investigation process, the distinct role of ecclesiastical institutions in Greece regarding land acquisition and the defects and malfunctions within Greek Land Administration System are presented. The paper concludes with the authors’ suggestions for addressing similar real estate property situations concerning land disputes.