In this paper, we explore a new avenue to a natural explanation of the observed tiny neutrino masses with a dynamical realization of the three-generation structure in the neutrino sector. Under the magnetized background based on $T^2/Z_2$, matter consists of multiply-degenerated zero modes and the whole intergenerational structure is dynamically determined. In this sense, we can conclude that our scenario is favored by minimality, where no degree of freedom remains to deform the intergenerational structure by hand freely. Under the consideration of brane-localized Majorana-type mass terms for an $SU(2)_L$ singlet neutrino, it is sufficient to introduce one Higgs doublet for reproducing the observed neutrino data. In all reasonable flux configurations with three right-handed neutrinos, phenomenologically acceptable parameter configurations are found.
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