My favorite Japanese bread is mentaiko pan. Mentaiko is pollack roe that has been cured in salt and seasoned with dried red chili peppers. At home we love mentaiko raw with a bowl of rice. It can be toasted on the outside and left raw inside for an umami-rich dish with sake.
The Japanese have brilliantly come up with putting into a small baguette with some butter and toasting it. Whenever I go into a new bakery it is the first thing I look for. Not all bakeries in Tokyo have it, so if you come across it, I recommend highly picking one up.
My commute into Tokyo takes me through Shinjuku station. The South Exit area has been under construction for a long time and has recently opened up under the new bus terminal. For me, this is the best mentaiko pan I have come across in the city. It opens at 8 a.m. and this is a great way to start the day.
Le Bihan is originally from Bretagne and dates back to 1913. It has many more stores in the Kansai region. Le Bihan, also has branch in Shinjuku Odakyu depachika, Ikebukuro Seibu, and Kita Senju Marui.
Shinjuku Station South Exit
Shibuya-ku, Sendagaya 5-24-55, NEWoMan Shinjuku 2F (inside the station gates)