Hands down the number one pick. A storied Soto Zen Buddhist temple surrounded by lush public gardens set amidst the towers of modern Tokyo makes this an easily accessible location for zazen meditation in the temple or a private urban session on your own in the gardens.
Morning sessions available every weekday starting at 7:00am sharp. It is a 3 minute walk from the Hiro-O Station on the Hibiya Line so is very central and easy to get to.
One of the city's best museums also has one of the most beautiful traditional Japanese gardens. Arrive at opening and find a quiet corner to enjoy a private meditation practice in this extraordinary hidden gem.
An inner garden surrounded by a beautiful park in the heart of Tokyo offers many locations for a quiet session meditating by oneself.
A temple in Kamakura. It takes about 60 minutes to get there from Tokyo Station but is worth the trip--18 temples and magnificent, 1000 year old gardens await. Zazen is offered twice a week.
Though not very central or traditional in appearance from the outside, this temple has zazen sessions every Saturday evening for beginners and on the first Sunday of every month for non beginners.
Though the temple main hall was built in 2001 (and therefore doesn't have the old feel some are looking for), this temple has the advantage of offering zazen sessions for the public multiple times a month and it is only a 10 minute walk from Shinjuku Station.
Kadampa Meditation Centre Tokyo teaches meditation in the heart of Tokyo at the Be Yoga studio.
A peaceful and quiet place in the heart of the city to reflect on life and death amid the graves of lives gone past.