If you are in such a situation, here is what I recommend you can do:
Make sure you have your fingering and pedaling written in (at least for 4 measures at a time). Practicing organ piece without the predetermined fingering and pedaling will make your playing very insecure, unpredictable, and not fluent.
Play slowly only 4 measures at a time. If you make mistakes, make a mental note of them and start practicing these 4 measures one more time. Fix the mistakes and aim for at least 3 correct repetitions in a row (5-10 repetitions if you are really serious about your progress).
Practice separate voices or parts first. Don't attempt to play two voices unless you can play solo lines slowly but perfectly repeatedly. Only then practice all available combinations of two voices. If you did the previous step honestly, then these two voices are going to be just a little more difficult but not out of reach.
The same holds true with playing combinations of three voices - do the two parts first. In a four-part piece, remember to play all four parts together only after you did all these preparatory steps.
You can also check if the piece you are working on is not too difficult for you at the moment. Try to play it at 50 % slower tempo than a concert speed. If you make more than 3 mistakes in one system while playing slowly - there is a good reason to believe that you need to take an easier piece for practicing now and work on improving your organ technique.
Apply these tips in your organ practice today. They really work. But don't expect fast results. Instead celebrate each conquered four-measure fragment. Then little by little you start putting them all together and your piece will begin to sound much better.
By the way, do you want to learn my special powerful techniques which help me to master any piece of organ music up to 10 times faster? If so, download my video Organ Practice Guide.