Although new classifications for neuroendocrine tumors were established by the World Health Organization, the current procedures and terms used in pathology laboratories are not known. A Web-based questionnaire was distributed to 491 institutions affiliated with the Japanese Society for Cancer of the Colon and Rectum, and 150 participated. The questionnaires included questions regarding routine pathological reporting, staining, and assessment of neuroendocrine tumors. Next, the time taken to assess Ki-67 index and mitotic count according to recommendation was evaluated to determine its feasibility. Most laboratories recorded diagnostic term, depth of invasion, size, lymph-vascular invasion, Ki-67 index, and mitotic count. However, only 32.2% reported tumor stage. Chromogranin A and synaptophysin were common neuroendocrine markers. D2–40 and elastica stain were frequently used to confirm lymph-vascular invasion. Only 62.1% counted more than 500 cells for the Ki-67 index, and only 17.0% counted more than 50 fields for the mitotic count, as suggested by the recommendations. Median time of 7 cases was 18.0 and 27.3 min to assess mitotic count in 50 fields with Ki-67 index in 500 and 2000 cells, respectively. For more standardized pathological reporting, education about standardized staging systems are needed in Japan. Practical and standardized procedures for mitotic index and Ki-67 index are also required.