This study aims to determine problems of the damage investigation system of aquaculture products resulting from natural disaster and to deduce improvement plans for such problems. The main problems revealed from this study were as follows: 1) detailed damage investigation is carried out only by one particular organization, 2) for aquaculture insurance subscribers another detailed damage investigation is conducted to reveal the causes of natural disaster by a joint investigator team formed according to a different legislation with a different purpose, 3) damage investigation is usually suffered from lack of labor, budget and time due to the restriction of natural damage to a certain period of season leading to the absence of quick reaction capability for irresistible natural disasters, and 4) there are no specified procedures and protocols for deciphering causes of a natural demage. The improvement plans to find solutions for such problems are as follows: 1) for the investigation, the object, method and role of the investigation organization should be clarified by improving the present legislation, 2) investigation methods for determining the demage causes should be systematized by making a manual to minimize disputes, and 3) supports for the investigation organization should be institutionalized to guarantee sufficient budget and manpower. Under the present circumstance with continuous natural damages, smooth procedures of damage compensation would lead to the management stability of aquaculture farms.