You were informed by your employer about your administrative case in the company, this is a formal notice that they are terminating your services. my question now is that did they ask you to formally explain your side what happend in this case? if they don't let you explain in writing, you were not given due process. Under the labor code, you need to be issued a formal notice to apprise you of the case and you need to explain. At any rate, as you said you admitted that you misappropriated company money and this is the price you have to pay for doing that- termination from service with just cause.
Now, if you did not signed anything and you are certain on that issue, your termination is deemed illegal and you can file a case before the NLRC to clear your name, otherwise you can not get a clearance and a certificate of employment.