In the first iaido exercise, my left kneel was always on the ground - appreciate some good advice from the seasoned iaido practitioners.
Depends on what is causing the pain. It can result from several different causes depending on how you are doing your kamae for your nuki.
Some people I know use knee pads. Others swear that all that pain is due to incorrect posture. Others say due to the floor being too soft. Others say due to the floor being too hard. Others say problem is the slippage of synthetic hakama on hardwood flooring and bunching of synthetic hakama under the meniscus of the knee when kneeling. Others say kamae is not high enough and others say kamae is too low.
Me, I wear cotton hakama on hardwood because soft floors give me knee problems. I take a relatively low kamae to keep bone on the floor rather than exposing the meniscus under the patella. Then, switch to a high kamae so that I only expose the meniscus for a short time. I also watch that I stay on my toes so that I do not expose the meniscus again. I also make sure that my weight is on my front foot when kneeling for Ipponme. Putting weight on the back knee also exposes the meniscus to damage and is improper posture anyway. I try to make sure that I am balanced so I do not put lateral pressure on the knee. This means that I must make sure that the heel of my front foot is in line with the heel of my back kneeling foot. Last, when I am starting to stand, I make sure that my knees are facing forward and my heels go down to the ground during that part where my knees are weakest to reduce the pressures on the knee just as I would use my legs overall in a "clean-and-jerk".
However, it still hurts my knees after a long practice due to loss of cartilage along my knee. I don't think that can be helped except for knee joint replacement.