We report an extensive search for Lyman-alpha emitters (LAEs) at z=6.5 in the Subaru Deep Field. Subsequent spectroscopy with Subaru and Keck identified eight more LAEs, giving a total of 17 spectroscopically confirmed LAEs at z=6.5. Based on this spectroscopic sample of 17, complemented by a photometric sample of 58 LAEs, we have derived a more accurate Lyman-alpha luminosity function of LAEs at z=6.5, which reveals an apparent deficit at the bright end of ~0.75 mag fainter L*, compared with that observed at z=5.7. The difference in the LAE luminosity functions between z=5.7 and 6.5 is significant at the 3-sigma level, which is reduced to 2-sigma when cosmic variance is taken into account. This result may imply that the reionization of the universe has not been completed at z=6.5. We found that the spatial distribution of LAEs at z=6.5 was homogeneous over the field. We discuss the implications of these results for the reionization of the universe.