Even at restaurants, it is common to have to pay at the cash register after your meal – wait-staff will not take money or credit cards from you at your table. You have to get up and queue at the cash register.
At the cash register, hand the bill/check to the person and then place your cash or credit card in that shallow little tray on the counter in front of you – do not hand cash or credit card directly to the person.
They, though, will hand your cash change or credit card back to you directly.
And remember, NO TIPPING! It’s not expected, and if you leave money on your table, they will assume you have accidentally forgotten it and and will chase after you to return it to you.
Japan Tourist Tips 