LEAVE IT TO THE Japanese—the people who many claim improved whiskey—to master the art of mixology. During past visits to Tokyo, I’d peer jealously over hotel highballs into the city’s neon nights knowing that somewhere out there better libations were being poured to well-connected salarymen in well-concealed night spots. These bars, which I’d heard mentioned with deep reverence over the years, always seemed out of my reach—not just because I didn’t know where to go, but because Tokyo is famously tough for visitors to navigate. Major roads are marked in English, but many of the smaller side roads don’t have any signs and in my experience only about one in every 10 passersby speaks English. This time I came prepared. An old pal put me in touch with Shinji Nohara, a former food writer, who sometimes works as a gastronomic guide for guests at the Conrad Tokyo, where I was staying. Mr. Nohara, also known as the Tokyo Fixer (so reads his Twitter handle), specializes in leading out-of-towners to the city’s hidden taverns. “Tokyo has 16,000 bars, most of them tiny,” Mr. Nohara said over a round of freshly squeezed juice with carbonated awamori—a sweet Okinawan liquor distilled from yeast and rice—at the start of our three-night bar crawl. “I’ll never see them all because someone is always starting something new.” Here, just the tip of the hand-carved ice cube, as it were.

Martha Photo: Jeremie Souteyrat for The Wall Street Journal

For the Vinyl Aficionado

In the trendy Ebisu neighborhood, the entrance to Martha is a battered wooden door illuminated by a sign that simply says “bar,” set in an even less promising cinder-block wall. Inside, the lights were dim and couples were huddled around tiny tables while the gray-haired DJ/owner was busy curating the soundtrack from the thousands of LPs lining the walls. All the music seemed much older than the 18-year-old Yamazaki single malt on offer, if not quite as precious (ABBA, Leonard Cohen and a Japanese Beach Boys cover band were all represented in the collection). Mr. Nohara advised me against making requests. “He’s got his own way of doing things,” he warned, pointing to the D.J., whose expression evoked a priest more than it did a spinner. “You’ll be thrown out.” Before leaving, we bowed gravely to the turntable master. He returned our bow. I guess I can come back. (1-22-23 Ebisu Shibuya-ku, martha-records.com/martha)

Bar Yamamoto Photo: Jeremie Souteyrat for The Wall Street Journal

For the Naturalist

Not far from the rowdy night spots of the Roppongi district, Bar Yamamoto is discreetly tucked away on a quiet side street. It’s a small, bare-white-walled room with just eight bar stools curving around a countertop fashioned from a 500-year-old slab of oak. Behind the bar, stands the owner, Gen Yamamoto, who, with shaved head, black tie and white jacket blends right into the minimalist surroundings. Mr. Yamamato serves you four or six seasonal cocktail “courses,” with drinks arriving in a variety of delicately cut glasses, etched with leaves and plants, made from his design. Our courses included Spanish gin mixed with fresh ginger and, for “dessert,” ground pumpkin and sesame seeds blended into Yamazaki whiskey single malt. Reservations recommended given the limited seating (Anniversary Building 1F, 1-6-4 Azabu-Juban, Minato, genyamamoto.jp).

Wall Photo: Jeremie Souteyrat for The Wall Street Journal

For the International Jet Set

We were wandering all over the posh Minato district’s Aoyama shopping complex until we found an unmarked handle-less utility door next to the Costume National store. Beyond the door is Wall, a tennis court-sized lounge with a lush, brightly illuminated vertical garden behind the bar where black-shirted barkeeps mixed elegant cocktails for moneyed expats. I’ve had better caipirinhas, so next time I’ll know to go for the Hibiki whiskey chilled by a hand-chiseled orb of ice the size of a golf ball (5 Chome-4-30 Minamiaoyama, cnac.jp/wall).

Rage Photo: Jeremie Souteyrat for The Wall Street Journal

For the Night Owls

Amid the neon lights of the Ginza district, we stepped into the elevator of an anonymous office building and pressed the third-floor button—the only one without a sign—and ascended to Rage, a 14-seat bar lined with rare aged-whisky. I was the only tourist and, despite the bar’s name, the other patrons, local businessmen just off work, did not seem particularly consumed with rage. I sank into a comfy leather chair and watched the three bartenders—yes, that’s a 3-to-14 ratio of staff-to-patrons—work their craft, mixing up ingredients you don’t often see at a bar, such as green tea, sage and sakura berries, until 5 a.m., closing time (8-5-24, Chuo-ku, 3F, 81-3-5467-3977).

Wodka Tonic Photo: Jeremie Souteyrat for The Wall Street Journal

For the Slavophile

Wodka Tonic is a subterranean tavern on a quiet lane behind the bustling streets of the Nishi-Azabu business district. It’s decorated with such elaborately carved woodwork that you might swear you were in Eastern Europe save for the 1,000-plus bottles of whiskey lining the cabinets. I ordered a Moscow mule, made there with fresh ginger. It was exquisite. When I tried to bum a cigarette from one of the salarymen at the bar the waiter rushed over with a whole pack and a lighter—the sort of service that reminded me that I was, indeed, far from Eastern Europe (Tamura Building B1, 2-25-11 Nishi-Azabu, Minato, wodkatonic.tokyo).