Well, for this problem I can see that, for starters, you need to enforce more secirity-driven policies in your office, specially when dealing with payments.
You should have a CCTV system installed, with various cameras recording, this should at least include the reception, desks where money is left and any place where clients transit.
Second, you should ask payments to be made via wire transfer to an institutional bank account, or via check given that you can check for risks accepting them.
Cash money should be handled by just one person and be kept inside the office only in one cash box, having registers of when it was opened and how much was taken/deposited, you should try to have as less cash as posssible on the office, having most of it in the bank or a security vault.
Did I mention CCTV? you really should have it installed.
Thats all I can say by now.