Liver cancer is one of the most frequent cancers in Europe and Greece. An increase in specific risk factors, such as metabolic syndrome and obesity, has been observed in Greece. Therefore, exploring temporal trends of liver cancer incidence and mortality is crucial. This study aims to assess the “burden” of malignant liver tumors (MLT) in Crete, Greece, in terms of incidence and mortality rates, and identify the high-risk areas on the island (i.e., municipalities), to suggest public health measures. Data were obtained from the Cancer Registry Center (CRC) and included all cases of MLT for the period 1992–2013 in Crete. Age-standardized incidence rates (ASIR), age-specific incidence rates (ASpIR), age-standardized mortality rates (ASMR), and age-specific mortality rates (ASpMR) were estimated. For the study period (1992–2013), incidence and mortality showed an increasing trend. Mean ASIR was found 15.3/100,000/year and mean ASMR 8.6/100,000/year. Age groups 65–69 and 75–79 years among men presented the highest rates of (ASIR = 39/100,000/year) and among women age groups of 75–79 and 80–84 years a mean ASIR (22/100,000/year). The five-year survival rate of MLT was 50% and the ten-year survival rate was 47% for both genders. Risk factors that were identified included personal history of cancer, family history of MLT or other cancer, degree of relationship, smoking, and obesity. Some municipalities of Crete were found to be high-risk areas for MLT, while differences were detected in incidence and mortality rates, and annual rate change among them. Estimated variation indicates further increase probably due to the lifestyle of the residents, economic crisis, and inadequate preventive measures.