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We define the Frobenius morphism of certain class of noncommutative blowups in positive characteristic. Thanks to a nice property of the class, the defined morphism is flat. Therefore we say that the noncommutative blowups in this class are Kunz regular. One of such blowups is the one associated to a regular Galois alteration. As a consequence of de Jong's theorem, we see that for every variety over an algebraically closed field of positive characteristic, there exists a noncommutative blowup which is Kunz regular. We also see that a variety with F-pure and FFRT (finite F-representation type) singularities has a Kunz regular noncommutative blowup which is associated to an iteration of the Frobenius morphism of the variety.