I got in trouble with my ISP, when I was new, becuase I didn't know it was bad. I was telnetting and used the portscanner for places to log into. The ISP wasn't even understanding. They shut me off and it took tons of work to let me back on. I hadn't even done anything else. There rules don't even say you can't, they just say no illegal activity. Why didn't they call and explain and say not to do it again. I'm rattling My advice like everyone elses, is confess. It is better to confess before he finds out than when he confronts you. You might try somthing like this:
You: Is portscanning illegal by company policy?
Boss: Yes, Why?
You: I'm sorry, but I didn't realize it, and I portscanned our server. I won't do it again.
Then you would would explain why you were portscanning. Of course, if you are lieing to us abou it, it might bring out the fireworks.