Assuming you're in Tokyo, no. I've never been whisky shopping in Tokyo.
In Osaka, yes. I know of a couple of extremely good places with the best prices you'll see. No idea if they're still open, however.
If Tokyo is anything like Osaka, you'll want to find a family-run warehouse-type liquor shop out in the suburbs. They will not be located anywhere near the city center (cheaper rents, cheaper liquor). In my case, when NOVA set me up in one of their shithole, overpriced "furnished" 1k units in the middle of fucking nowhere, they also gifted themselves a number of extremely bad, hungover lessons because right down the street, in the backstreets along the local train line, was a massive liquor distribution warehouse run by an old family and they had EVERY-FUCKING-THING and for far cheaper than any department store or even standard liquor shop in town.
All of a sudden I could afford to drink classy and get all the stuff I could've never afforded back home. Whereas I was chugging Canadian Mist and 7-Crown with Diet Coke and ice, now I could afford to mix Johnny Walk Black (1900 yen for 1L), Glenlivet and Macallan 12 (maybe 2500 yen?) with Diet Coke and ice. That's right, I did that. Shit, they had bottles of Johnny Blue for 8800 yen. Rows and rows of sake and shochu and a decent wine selection, too. Even better, they had a massive selection of snacks, and all the kinds of Japanese snacks I absolutely love for drinking solo (arare, saki ika, nori ten, etc.). It was like a one-stop-shop for alcoholics. Once in a while, when I'm back in town, I go walking in the old neighborhood and pop into the warehouse for the nostalgia. But then I realize that the old timers who used to run the register are probably dead and the little girl who used to help her grandparents and stock shelves is probably married with kids and not having sex anymore, and then I feel old and then I get angry and then I just go back to my hotel and drink myself to sleep hating Osaka and dreaming about hopping on the shinkansen tomorrow and going somewhere else.
If you have free time, just go walking around any nice suburb, and look for the warehouse with the alcohol sign/flag and pallets upon pallets stacked up out front. Should do fine there.