We do negotiate prices sometimes in appropriate situations!
In most B2C cases, Japanese consumers don't negotiate prices and most shop clerks don't have the power to lower them, but in some situations we do!
When we go buy electronic appliances, PC's, tablets, etc. at some mass merchandise stores/outlets such as Yamada Denki (LABI), BIC Camera, Yodobashi Camera, etc., we usually do negotiate. They declare that they will make their best efforts to lower the prices to the lowest level when customers find better prices/conditions elsewhere,
and we actually do negotiate sometimes, therefore the prices presented at their stores are usually higher than the lowest level so that they may be ready to discount and we may enjoy successful price negotiations. This means prices should be negotiated!
The best way for us to present such better prices is to use the kakaku.com website (only in Japanese language, though) if you can read and input in Japanese. Even though you may not understand Japanese enough, you can put in the English name of a product in its search box as some products' names are in English.
Another place when price negotiations often do take place is Ameyoko （アメ横） in Ueno （上野） in the Tokyo area. For Ameyoko, see the website below:
Some websites suggest you say "Benkyo Shite Kudasai" (literally meaning "Please study" but its idiomatic meaning is "Please give me a discount), but this expression is old, so we nowadays seldom use it, so it's not recommended for foreign visitors as well. The way we usually negotiate is to ask "how much if we buy 2 or 3?" as in other countries. People visiting Tokyo from a local district often say "I've come here all the way from ..... , so discount, please!!!" Therefore, you may as well say "I am from .... all the way, so discount, please." Many vendors in Ameyoko don't speak English, but they somehow understand easy English, so I suggest you use easy words and gestures by putting your hands together as if you were praying (for a discount). lol