If I get time enough (sorry, unlikely this week), I'll see if I can find the pertinent laws. In the meantime, I'll let you know what my contract says about that.
In my contract, there is no direct mention of "sikikin", but there is "hoshoukin", which is basically the same.
My hoshoukin incurs no interest during my stay at my apartment.
I can not use my hoshoukin to pay my rent while I stay here.
blah blah blah
More to the point of this thread, the following will be deducted from my hoshoukin when I leave regardless of the length of my stay.
Housecleaning Fee 38,000 yen
Fee for Changing the Locks 15,000 yen
Make sure you read your contract before you press your seal to it, because once you do, it's legally binding!