Here are the top universities in Japan according to the most recent rankings from various sources:

1. **University of Tokyo**: Consistently ranked as the best university in Japan, it is also one of the top universities in Asia and globally. It is renowned for its research outputs and academic excellence【14†source】【16†source】.

2. **Kyoto University**: Known for its strong emphasis on research, Kyoto University ranks second in Japan and is highly regarded in Asia and globally【14†source】【16†source】.

3. **Osaka University**: This university is well-regarded for its contributions to research and its comprehensive academic programs. It ranks third in Japan【14†source】【16†source】.

4. **Tohoku University**: Located in Sendai, Tohoku University is noted for its research achievements and educational quality, consistently ranking within the top universities in Japan【15†source】【16†source】.

5. **Nagoya University**: Known for its research, especially in the sciences, Nagoya University is another top institution in Japan【16†source】.

6. **Kyushu University**: This university is known for its strong academic programs and research initiatives, ranking among the top universities in Japan【16†source】.

7. **Hokkaido University**: Located in Sapporo, Hokkaido University is noted for its research and comprehensive academic offerings【16†source】.

8. **Keio University**: A prestigious private university in Tokyo, Keio University is recognized for its academic excellence and influential alumni【16†source】.

These universities are highly regarded for their contributions to education, research, and their impact on both the national and international stages. For more detailed information on the rankings and specific metrics, you can refer to sources like Times Higher Education and EduRank.