To learn about these principles join a dojo and ask your instructor.
The Ninpo Ikkan
The law of the Ninja is our primary inspiration.
One way to punch in Ninjutsu is to follow through with the power and after a strike the hand appears to be "stuck" to the target. This allows the full weight of the punch to be directed into the attacker. The disadvantage of not pulling the hand straight back is it could be grabbed or caught. We practice wrist escapes and reversals a lot and this should not be a disadvantage but an advantage. There is a saying in Ninjutsu, "If someone grabs you, you"ve got them!".
Ninjutsu is a very tactile art and then best way to train is with a training partner. Being a good training partner is a skill in itself and your job as a training partner is to provide a positive learning experience. When first learning a move it is often necessary to slow the attack down, this is not because the technique doesn"t work but because you need to learn how to perform the technique properly. The training partner needs to provide the correct speed and resistance to allow the practitioner to learn the move. If the training partner provides to little speed and resistance then learning of the technique is affected. If the training partner provides to much speed and resistance then learning could also be affected (both the practitioner and the training partner are in danger of getting hurt in this scenario too). If the training partner is skilled enough to provide just the correct amount of force and speed then learning takes place in a safe environment. As the practitioner get better at the technique the training partner can use more force and speed to allow the practitioner to "master" the technique.
Three stages - techniques are done in three stages to use the body weight as a weapon as well as putting you into a better more advantages position. This concept can be used against attackers who are bigger and stronger than you are. The concept of san shin came from fighting in armour. It is often used with the go-dai or 5 elements concept.
Leading with the knees
Fudo ken (an immovable fist) is a punching move and can be performed in a range of ways. One way is where you do not rely on even, stable ground but instead uses body weight. If fighting on mud, sand gravel or slippery ground using the back foot to "push off" could cause you to slip and slide. Instead push your hips forward until you have to take a step - Hatsumi Sensei calls this leading with the knees.
"Old Tree - Young Tree"
There is an old Japanese saying that a tree is at its most vulnerable at the end of its life and at the start of its life and this is the case for many things in nature and in Ninjutsu. If someone tries to punch you they are at their weakest at the start and end of the punching movement. If you deliver your defensive move at these key points then the techniques will be more effective.
"Ninjutsu is like life"
Like life Ninjutsu is ever changing and you are only as good as the last time you training. Unlike most martial arts gaining a grade or belt isn"t enough. You have to keep on top of your training. As you improve your techniques will change - nothing stays static and you need to embrace this principle not fight against it.
"The nail that sticks out gets hammered in"
An old Japanese saying that is true for the Ninja more than most. Sometimes its best to just "fly below the radar" and not be noticed. One saying my instructor told me and it has put me in good stead is "you have two ears and one mouth and you should used them in that ratio"