Many better hotels offer a Japanese breakfast set - sometimes in their Japanese restaurant, sometimes as an option in the breakfast area, and sometimes by room service.
Business hotels often offer a more typical sort of Japanese breakfast consisting of onigiri, some sort of soup, salad, toast and/or other types of bread, maybe eggs (though often made from powder)... Varies by hotel what and how much they offer.
Are you up to grilled fish, raw egg, natto(fermented slimy soy bean that may smell a little), yamaimo(slimy grated potato that may make your lips itchy), etc.?
If not, you might try bf buffet at any decent large hotel where they have Japanese & western bf food items, juice/milk/coffee/tea for ~2,000yen, if not staying there.
The Imperial Hotel at Hibiya serves a great traditional Japanese breakfast.
¥2000 per person for a hotel buffet or Japanese set is a bit of a stretch I think unless you are talking business hotel or just a bit above. For reference in Tokyo...
Imperial Hotel Tokyo Japanese breakfast ¥2940 in Nadaman, buffet ¥3360 in Imperial Viking Sal.
Peninsula Tokyo Western style breakfast ¥3800, Japanese style ¥3900.
Westin Ebisu breakfast buffet ¥3600.
Grand Hyatt's French kitchen western and Japanese breakfast ¥3700.
it's not too bad if you avoid the strong tasting mackeral (Mrs B loves it), and if you ask for your egg to be cooked. Miso - yum.
All others have given you good advice. Here's one more, a little different and much cheaper. If you can find a very popular chain restaurant called "Yoshinoya" they serve typical Japanese breakfast, miso soup, grilled salmon, natto (optional), raw egg (optional) and a few other items. If you do not mind casual atmosphere, I recommend this restaurant.
Other than hotel's "fancy" and very nice breakfasts, family restaurant chain have good typical Japanese traditional breakfasts.
Denny's (Please click green "メニュー menue" bar.)
Actually, if you want to have the breakfast that most Japanese people eat, then suggest 7-11 for bread rolls or Onigiri rice ball. Wash it down with some vegetable juice in a tetra box.
one of the most expensive, "traditional" breakfast in Kyoto--
Asa-gayu/Uzura-gayu at Hyo-tei, Nanzenji.
around 5,000 yen.
more normal breakfast would be www.yoshinoya.com/menu/morningset/index.html (300-500 yen)
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