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Interception loss (<i>IL</i>) by the forest canopy removes a substantial quantity of rainwater within forested ecosystems. The large-scale unmanaged Japanese coniferous plantations with high stand density (<i>SD</i>) in Japan raise concerns about an additional increasing <i>IL</i> as a result of a new influential factor of dead branches under canopies. Thus, evaluating the usage of <i>IL</i> estimation models is vital to regulating the water and environment in such coniferous plantations. This study aimed to examine the applicability of the reformulated Gash analytical model (RGAM) to unmanaged coniferous plantations with high <i>SD</i> laden with dead branches. We established two plots (P1 and P2) laden with dead branches under the same <i>SD</i> of 2250 stems ha⁻¹ but with different numbers of dead branches (56 vs. 47 branches per tree) in an unmanaged Japanese coniferous plantation. Results demonstrated that a large difference was found in canopy storage capacity (<i>S</i>) in P1 and P2 (3.94 vs. 3.25 mm), which was influenced by the different number of dead branches; therefore, the <i>IL</i> ratio to gross rainfall differed considerably (32.7% in P1 and 26.7% in P2) regardless of the <i>SD</i> being the same. The difference in <i>S</i> enables the RGAM to reflect the influence of dead branch structures on <i>IL</i>, leading to an acceptable RGAM performance for both P1 and P2 (“fair” <i>IL</i> relative errors: −20.2% vs. −16.1%) in the present study of unmanaged coniferous plantations with high <i>SD</i> laden with dead branches.