This study examined the empirical differences between the tendency to omit items and reading ability by applying tree-based item response (IRTree) models to the Japanese data of the Programme for International Student Assessment (PISA) held in 2009. For this purpose, existing IRTree models were expanded to contain predictors and to handle multilevel data. The results revealed that Japanese students were more likely to omit open-ended items than closed-ended items, despite the fact that average item difficulty of the open-ended items was lower than that of the closed-ended items. Variances of the omission tendency were larger than those of reading ability, especially for open-ended items. Female students tended to omit more closed-ended items but fewer open-ended items than males, but the female students showed higher reading ability on average. Use of control strategies was negatively correlated with the difficulty of reading items and with the tendency to omit open-ended items. After controlling for other student properties, use of memorization strategies was negatively correlated with reading ability, which was opposite to the simple correlation. The results clearly show that the omission tendency can be differentiated from reading ability. School-level means of socioeconomic status and teacher stimulation explained more variance of both the omission tendency and reading ability than student-level properties. This implies that school-level interventions will be more effective than student-level instructions.