Unlike many western countries, tipping is not customary in Japan. Service workers do not depend on tips and tipping is not recognized as a way to show appreciation. Rather, people would most likely turn down tips, and some might even consider it rude.
Japanese people will give excellent customer service without a tip. If you are absolutely inclined to tip, it will be appropriate to put cash in an envelope instead of pulling out money from your wallet and giving it directly. However be ready to be declined, as many companies restrict employees from getting personal gifts from customers.