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Assuming you don't have a serious condition of some kind, it's likely that you're not ready for that long of a run. So, cut your time back to 3 minutes. If you can run that without the cramps, that is great. Stick with that time for a while to let your body get used to it. Run heavy/light. That is, run 3 minutes one time and 1.5 minutes the next. The light day of half the distance will allow your body to recover from the 3 minute run. Sports doctors say we need at least 48 hours for recovery. Then follow the 10% rule in increasing your time. That is, make small increases in your time such that you don't have the cramps, and stay at each new level until you feel comfortable with it. If your cramps return, drop back to the previous level and repeat that for a week or two. Cramps are one way your body talks to you and tells you it can't handle the stress you're giving it.
Here is a page that explains heavy/light and the 10% rule.
http://runninginjuryfree.org/2008/08/coaching-running-on-internet.html
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Posted by darrenchambers1981
Basically it has been a while since I have done serious exercise although i have alwasy suffered with this even from a very young age.... I have started running again and find I can go no longer than 5 moins without having excruciating pain in my stomach, it has been hindering my attempts to get fit!! the pain can last up to 2 hours even after only running (at very slow pace) for 5 mins.. I have tried eating less salt in my diet, doing less vigorous exercise to build fitness slowly but nothing seems to help!!