Study your ninjitsu, or ninja, reference material. Before you do any hands-on practice you need to read the history and theory of ninjitsu so that you understand its goals and philosophies. Every maneuver and technique you learn needs to be incorporated with the theory and philosophy to create a whole. Warrior-Concepts-Online and The How to be a Ninja are two websites where you can begin your search for references, both theoretical and practical, for learning ninjitsu on your own.
Practice drills and exercises as listed in your references. Ninjitsu, like any martial art, recommends you perform regular drills to both strengthen your body and program your muscle memory. You need to drill and practice thoroughly so that you can respond on pure reflex. If you see your opponent's shoulder move so that you know a punch is coming, you need to know how to counter it and to react swiftly. Make sure that you drill every day, even if it is only for 20 minutes in front of a mirror, to see how your technique looks.
Practice with a partner. Once you are familiar with techniques, you need to practice with a partner. Choose a certain technique and practice it at half speed, never actually striking your partner unless he's properly padded. Add drills with a partner as often as you can, ideally three days a week. If both you and your partner want to go full speed without hurting each other, put in mouth guards and pad your hands, shins, heads and possibly torsos and spar in a safe, controlled environment. This allows you to become familiar with maneuvers.