I have often heard that yes it does, and no it does not. The fact is that densho (transmission scrolls) do exist detailing the skills used in war and defense, including hand to hand combat. Does this qualify it as a martial art?
From the standpoint of "is it a martial art" I think the answer is most definitively "yes." Many of the techniques it practices are very fitting in with other contemporary "martial arts." It teaches hand-to-hand combat and techniques such as dive rolls and breakfalls, among other things, that are commonly found in other martial arts. I can't really think of anything that would keep it from being considered a "martial art."
On the other hand, that's an easier question than whether it should be considered a traditional martial art. That's a substantially more difficult question, but not one that really detracts from whether it should be considered a martial art in its current form.
For some reference, Ive been training in a ninjutsu school for a couple years now.
From what I have gathered is that the ninjutsu aspect of the art is more of a state of mind rather than specific martial schools. The ninjutsu aspect focus's on getting out of line of sight and distracting the opponent. In fact the only unique ninjutsu kata i have found teaches the person to distract and invade the opponent.
Most of the other techniques are very jujutsu like.
This is a good read on the school i attend. http://blog.bushinbooks.com/archives/11
If we assume, as others have described, that arts such as Kyudo, Kendo, Kickboxing, Kumdo, Escrima, etc. are martial arts, then we need to give a broad definition to the term. Martial Arts could, therefore, be described as:
In this way, we include under the banner 1.) combat sports (which we must acknowledge as, at the very least, being derived from warrior virtues), 2.) philosophical pursuits of war (Heiho/tactics, for instance, or the zen aspects of Kyudo without including pursuits such as Shodo or tea ceremony), and 3.) weapon arts (to not exclude those arts that are purely related to the development of a weapon skill, such as Iai, whether or not they are viewed, correctly or incorrectly, as practical). Further, we exclude any need or demand for any moral guidance through the art, allowing both those arts dubbed
Then, if we accept this definition, we must accept ninjutsu as a martial art, since it is inclusive of tactics, weapon skills, and those traditionally warlike aspects of effectively eliminating an enemy.
I've come to a new realization regarding ninjutsu, which I feel I need to share. Please forgive its depth. Going through the shoninki, bansenshukai, and shinobi hiden (along with new translations) have led to a new understanding. This too is likely to change.
Ninjutsu is an erroneous name; the art is better written 忍ノ術, read "Shinobi-no-Jutsu", the arts of the shinobi. The art, or rather collection of skills, is not combative, and consists of a series of skills related to their abilities:
Now, this is shinobi-no-jutsu, or what we commonly call ninjutsu. Saying that it is a "martial art" is a bit like saying that a KGB agent living in the US during the cold war was a "soldier".
As far as combative skills, it's likely that many had training, likely in some form known to their family or through affiliation.
I don't know if this is an answer, but I thought I should post the new information and add it for evaluation.
(Disclaimer, I train in Bujinkan Budo Taijutsu)
Nin "JUTSU". The answer is in the name. Wikipedia
Update Dr Kacem Zoughari discussing ninjutsu as an martial art.
Is there a unique [set of martial arts] for the ninja? Not in my experience. The basic weapon work (bokken, bo, tanto) is very similar to other "traditional" Japanese martial arts, and so is the un-armed stuff. What is different (but again, not unique) is the emphasis on "warrior combat" and "battlefield awareness" with an eye on surviving, not achieving an honourable death.
I would think it can definitely be considered an art because it evolves over time, and students who become teachers will favor certain techniques and skills, and will assimilate techniques and skills from other arts.
It also is not a closed system bound by unbreakable rules - IOW if you come up with a new technique or skill that works then you can incorporate it in. This in itself would mean it satisfies the definition of an art as opposed to a science or practice.
That means that a ninja can murder, steal and perform any low-moral acts.
To make an analogy to modern times, you can think of a ninja as a "bad guy" on the broadest of the sense.
Then "-jutsu" suffix means technique.
Therefore ninjutsu is basically a list of the technique used by bad guys without honor. Is this an "martial" art? I doubt it.
However, the technique used are probably effective, if all that you care is to do bad things (as opposed to knowing yourself, build a better society and so on).