  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.
