Background The Great East Japan Earthquake and subsequent tsunami devastated the northeastern part of Japan. Low back pain is thought to increase after a natural disaster and is related to various factors. The aim of this study was to examine the influencing factors of “Living environment” and “Subjective economic hardship” on new-onset of low back pain in the chronic phase for the survivors of the earthquake evaluated by a self-report questionnaire. Methods A panel study was conducted with the Great East Japan Earthquake survivors at 2 and 3 years after the disaster. New-onset of low back pain was defined as low back pain absent at the 1st period (2 years after the earthquake) and present at the 2nd period (3 years after the earthquake). Living environment was divided into 4 categories (1. Living in the same house as before the earthquake, 2. Living in a prefabricated house, 3. Living in a new house, 4. Others: Living in an apartment, house of relatives or acquaintance). Subjective economic hardship was obtained using the following self-report question: “How do you feel about the current economic situation of your household?” The response alternatives were “Normal”, “A little bit hard”, “Hard”, and “Very hard”. A univariate and multivariate logistic regression models were used. Results 1357 survivors consented to join this study. There was no significant association between new-onset of low back pain and living environment. There was significant association between new-onset of low back pain and “A little hard” (OR = 1.6, 95% CI = 1.07–2.40), “Hard” (OR = 2.2, 95% CI = 1.56–3.74), and “Very hard” (OR = 3.19, 95% CI = 1.84–5.53) in subjective economic hardship. Conclusions Subjective economic hardship was significantly associated with new-onset of low back pain in the chronic phase for survivors of the Great East Japan Earthquake.