There is widespread concern about declining literacy skills in recent young Japanese. The present study investigated how higher-level reading and writing proficiencies are underpinned by basic literacy skills in Japanese adolescents. From a large database of the most popular literacy exams in Japan, we retrospectively analyzed word- and text-level data for middle and high school students who had taken the exams during the same period in the 2019 academic year using structural equation modeling. We extracted main data for 161 students as well as six independent datasets for validation. Our results validated the three-dimensional view of word-level literacy (reading accuracy, writing accuracy, and semantic comprehension) and demonstrated that writing and semantic skills underpinned text writing and reading, respectively. The semantic comprehension of words affected text writing indirectly via text reading; however, it could not replace the direct effect of word writing accuracy. These findings, which were robustly replicated with multiple independent datasets, provided new evidence of dimension-specific relationships between word- and text-level literacy skills and confirmed the unique contribution of word handwriting acquisition to text literacy proficiency. The replacement of handwriting by digital writing (e.g., typing) is a global trend. However, the dual-pathway model of literacy development identified in this study suggests there are advantages in sustaining early literacy education by handwriting for the growth of higher-level language skills in future generations.