Only counting active (ie. working) directors, these are whom I would consider to be in the top tier (not in order):
Hirokazu Kore-eda
Kiyoshi Kurosawa
Hayao Miyazaki
Isao Takahata
Yoji Yamada
Takeshi Kitano
Seijun Suzuki
On the lower auteur scale there are Naomi Kawase, Takashi Miike, Masayuki Suo, Shunji Iwaii, Nobuhiro Suwa, Shinji Aoyama, Masaki Kobayashi, Koji Wakamatsu, Shinya Tsukamoto, Sono Sion and Mamoru Oshii. Reason why I put them under the lower echelon is because their works are less consistent than the directors above. Still, they have a number of standout works which make them "auteurs".