The results of earthquake damage certification (EDC) surveys are the basis of support measures for improving the lives of disaster victims. To address issues such as a limited workforce to perform EDC surveys and difficulties in judging the level of damage, a damage detection and level classification method for wooden houses using multiple convolutional neural network models is proposed. The proposed method, including detection, filtering, and classification models, was trained and validated based on photographs collected from EDC surveys in Uki City, Kumamoto Prefecture. Then, a software system, which deployed these models, was developed for the onsite EDC surveyors to detect damages shown in the photographs of the surveyed house and classify damage levels. The test results based on 32 target buildings indicate that the detection model achieved high recall in detecting damage. Moreover, the redundant detected regions can be precisely filtered by the filtering model. Finally, the classification model achieved relatively high overall accuracy in classifying the damage level.