Foreigners looking to cook in Japan may find the spice rack at their local grocery woefully lacking. A few aisles over you can choose between ten kinds of soy sauce, but if you want to find cumin it’s hit or miss. It makes sense, of course: Japanese food relies on a few staple flavors, while the whole of the rest of the world’s cooking offers much more variety. I couldn’t find mirin in most American grocery stores, so I wouldn’t expect to find anything outside the basics in Japan.
That said, there are some places you can pick up the lesser-used spices in Tokyo, even where you might not expect. Online stores are a given, though for me that requires way too much forward planning. I prefer to hit up the nearby department store Tokyu Hands, which boasts a surprising array of reasonably-priced (300-400 yen) bottles of spices and a decent selection of extracts in their kitchen section. MUJI and LOFT have food/kitchen sections, too, though I haven’t had consistent luck at either, so your mileage may vary too. Hanamasa, a restaurant wholesaler with a distinct yellow-and-black cow’s head sign, also has bottles of foreign spices–Thai, Chinese, Indian, and Korean at the one near me–in super size, if you’re going to need a lot of turmeric. Basement groceries at department stores, which are fancy pants and therefore have an aisle or two of foreign foods, are good spots to poke around too.
Happy cooking!