In this paper we consider possible mechanisms to generate small Majorana neutrino masses for active neutrinos in the scenario of gauge-Higgs unification, a candidate for physics beyond the standard model. We stress that it is non-trivial to find a gauge-invariant operator, responsible for the Majorana masses, which is the counterpart of the well-known SU(2)$_L \times$ U(1)$_Y$ invariant higher-mass-dimensional ($d = 5$) operator. As the first possibility we discuss the seesaw mechanism by assigning leptonic fields to the adjoint representation of the gauge group, so that a $d = 5$ gauge-invariant operator can be formed. It turns out that the mechanism leading to the small Majorana masses is the admixture of the Type I and Type III seesaw mechanisms. As the second possibility, we consider the case where the relevant operator has $d = 7$, by introducing a matter scalar belonging to the fundamental representation of the gauge group. Reflecting the fact that the mass dimension of the operator is higher than usually expected, the Majorana masses are generated by a "double seesaw mechanism."