Using scanning tunneling microscopy and transmission electron microscopy, we demonstrate the existence of antiphase boundaries between neighboring grains shifted by a fraction of a quintuple layer in epitaxial (0001) films of the three-dimensional topological insulator Bi(2)Se(3). Scanning tunneling spectroscopy and first-principles calculations reveal that these antiphase boundaries provide electrostatic fields on the order of 10(8) V/m that locally charge the Dirac states, modulating the carrier density, and shift the Dirac point by up to 120 meV. This intrinsic electric field effect, demonstrated here near interfaces between Bi(2)Se(3) grains, provides direct experimental evidence at the atomic scale that the Dirac states are indeed robust against extended structural defects and tunable by electric field. These results also shed light on the recent observation of coexistence of Dirac states and two-dimensional electron gas on Bi(2)Se(3) (0001) after adsorption of metal atoms and gas molecules.