Not really. Japan's "sunlight laws" make it really hard to go above around three stories or so, meaning that nearly all of Tokyo's skyscrapers are concentrated in a few hot spots with commercial zoning (Shinjuku, Marunouchi) plus a few mega-developments like Roppongi Hills where the developer could pull enough strings to buy a large chunk of land and bulldoze their way to an exception.

Of course, compared to Silicon Valley, even the suburbs of Tokyo are indeed densely packed -- but then, Tokyo also crams in something on the order of 7x more people into the same area.