We investigate the ground state structure of two-dimensional Josephson junction arrays consisting of Bose-Einstein condensates trapped by both a rotating harmonic potential and a corotating deep optical lattice with square symmetry. Monte Carlo simulations of the uniformly frustrated XY model in a wide range of the frustration parameter f reveal that the stable configuration of vortices for a simple fractional number f is a staircase structure, consisting of diagonal chains of vortices with periodic lattice of unit cells.