I am not sure what that is supposed to cover and when they pay it. When you rent a place in Japan, you need to pay four months rent up front. The rent, a fee the land lord, a fee to the agent that you used and a security deposit. When you first move in, the government will give you enough money for three of these. You have to pay the deposit, but you should get it back when you move out. It is fun when you pay all of these since nobody takes checks there and you need to get around 5 thousand dollars cash from the bank.
But you will be eating ramen ... It's a real meal there (and good).