Yes you do have to pay for garbage collection in Tokyo (the part I live in anyway), the price you pay for the special plastic bags you have to put your garbage in is the fee. It used to be free for everything, even big items, but not any more.
Here is an example of the prices from Mitaka City. As you can guess, one 5 liter plastic bag is not going to cost ¥90 to produce.
- Mini bags (5 liter) 90yen
- Small bags (10 liter) 180yen
- Medium bags (20 liter) 370yen
- Large bags (40 liter) 750yen
