Once you've ruled out the physical, talk with the school counselor. He needs to be aware of the problems your son is having. The school counselor may be able to give your son some individual time or include him in a small group. If you feel your son needs additional help outside the school, the counselor or your pediatrician can refer you to a therapist in your community.
You'll want to address this issue behaviorally as well. Think about your reaction to your son's complaints in the mornings. Do you give him attention when he complains about not feeling well? Do you take his temperature? Do you argue with him or try to cajole him into going to school? Once you are sure there is no physical problem, try ignoring his complaints. Every time he says something about not going, be very matter-of-fact and say, "We're leaving in 15 minutes ... We're leaving in 10 minutes ...," etc.
Also, give him positive attention and praise when he is getting ready without complaining. Set up a reward system for getting ready for school with no problems, with three pleasant mornings in a week earning the right to have a friend over to play on the weekend.