This is a tough question.  First of all I am not a medical doctor, but will be answering this question based on my experience as a classroom teacher.  I would make these suggestions to parents who had children that had trouble sitting for short periods of time or couldn't stay focused.

Start with keeping a journal on your son's behavior - the good, bad and the ugly.  Write down times, what he ate, when happened just before.  Ask him to explain what happened to make him to become fidgety.  Are there specific times during the day when his behavior is better or worse?  Are you noticing anything in his diet that is trigging good or bad behavior?  Are there activities where he is totally focused for long periods of time?  Does he have trouble sitting when he is alone?  Or just when there are distractions around him?  You want to look for patterns, so try to keep detailed accounts of what is going on.

You may want to take him to see his pediatrician.  Explain to the doctor your concerns and what findings you found by keeping a journal.  He may want to run some basic blood tests to see if there is any type of imbalance.  It may be lacking a vitamin or his blood sugar could be out of whack.  

Ask the school for help.  They probably don't take parent requests for teachers, but ask them to match your son up with the teacher best capable to handle him.  Describe the kind of person he works for or tries to please the most.  

Practice short periods of time sitting with him working on different activities.  It might be reading together, putting together a model, playing with legos, etc.  You can model this behavior for him.  Afterward talk about it.  Ask him if it was hard?  Why was he able to sit and stay focused?  What made him get up and want to do something else?  

The link below found on Education.com will provide some information explaining how boys brains develop.  This might give you a little more insight as to what is going on in your son's head.

Hope this helps.