Never spend more than a few minutes on any exercise or section of a piece that causes discomfort to any part of your body. Pain in the back, shoulders, and in the hands and wrists is common among organists.
If pain develops in tendons between wrist and elbow, discontinue practice for a few days and make sure you are taking a good Vitamin-B Complex supplement to rebuild the damaged tendon as soon as possible.
Remember--it is so much better to prevent than to try to cure!