Can an employer, if cash is missing, give me the option to pay back the money or they will press charges even though I didn't take anything?

I had a few thieves in my store that I couldn't identify. I wanted to ask for help, but was told that any cash shortages would result in my termination. I made up as much as I could out of pocket, but couldn't keep up, nor could I identify who the problem was. Now I'm being threatened with either repaying the cash or having charges filed against me.