Will Panacur cause diarrhea in my puppy?

My puppy is 11 weeks and 3 days ago was diagnosed with 'whip worms'. The doctor gave us panacur to help rid him of these worms. The first day I forgot his medication at work, yesterday night I gave him his first dose, today I misplaced his medication and when I got home from work he had diarrhea all over the bathroom. According to my fiance he had already thoroughly cleaned the bathroom twice and has probably went about 15 times today. It is very watery, no blood. I have found the medication but am afraid it will cause him to get ill again. I work at the vet clinic I take him to and am not able to bring him in until 9 tomorrow morning. Should I continue the medication or stop until he sees the doctor tomorrow? Can the whipworms cause him to be this ill? Also thought I would mention that he is eating and drinking water and isn't lethargic..