Jon Hass over at Warrior Fitness posted this excellent explanation of where strength fits into ninjutsu:
A common misconception that you’ll hear bandied about from dojo to dojo all across the world is that strength, and by association overall, general fitness, is not required. I think this has to do with a fundamental misunderstanding of how we train. In class, when practicing techniques, it is imperative to be as efficient in one’s movement as possible, and thus avoid using excess, unnecessary power (read – strength). In order to accentuate the study of distance, timing, angling, and space management, one must put strength on the back burner in the dojo to avoid powering through the movements and missing all the wonderful subtleties that taijutsu has to offer. However, in an actual conflict, you can and in fact, you must, use all your power, including strength, to survive. As Jack Hoban said in his interview here, “real fights are very physical – tiring and punishing”. Anyone who thinks physical fitness isn’t required in the traditional martial arts is really just kidding themselves.
Full article: http://warriorfitness.org/fitness-requirements-for-bujinkan-martial-arts-training/