In the most ancient of oldest books in the Restricted Section of the Library was a book detailing the oldest known human race known as...ninjas.
Long, long ago, two different group of people learned magic. Wizards and witches learned magic while ninjas learned signs and jutsus, controlling a inner stream of magic known to them as chakra.
Trained from as early as 7 to 8 years of age, they can graduate at any given time but majority being 12. Once graduated, they were considered to be adults and were given missions by their head of government.
They were trained from a early age to kill, to assassinate, to protect, to guard. They didn't bat a eye against blood, nor did they flinch when they were stabbed. It's not like they recommended the idea of killing others, but it was how they were brought up. Given that there was insane S-ranked criminals out there in the Hidden Continents, generation after generation of children were taught not to fear the idea of blood. Learn to face the pain, but don't seek or embrace it.
After learning the basics (Shadow Clones, Transformation, Replacement, Shuriken/Kunai Throwing, Chakra Theory), they are then separated into 3-man cells led by a higher- up, where they honed their individual skills on various types of ninjutsu.
All of them lived on a rather large island located to be near modern-day Japan, separating into individual nations based on elements.
5 of them were the most powerful, dominating over the rest: Konohagakure (Land of Fire), Sunagakure (Land of Wind), Iwagakure (Land of Earth), Kumogakure (Land of Lightning), Kirigakure (Land of Water).
Once upon a time, shinobi and kunoichi alike walked the earth with wizards. Healing techniques were shared among nurses and medical ninja, despite the large gap between the ninja who used wandless magic and those who required the need of a wand. Kages, powerful individual ninjas, were involved in the political affairs with the Outside, discussing and forming political alliances.
But soon, time would drive the two human races apart. Selfish wizards, those who wanted to hang on to their power and fame, would employ shinobi to assassinate others, sometimes their own friend.
The Kages finally snapped, after years and years of endless wars. One war would end only for another to take its place several years later. Truly, the term 'peace' is merely just a word. Peace never existed long in the Outside. The same could be applied to us wizards and witches.
Erecting a giant shield around their entire island, civilians and ninjas disappeared behind it, to no longer make outside contact. Time ran slower inside the shield. Its jutsu formula ever so complicated, it made its own climate in various regions and time slowed down. A decade would trickle by the ninjas as a century raced by the wizards. Civilians forgot there was even land outside of the shield. Memories wiped clean, they lived contentedly without modern technology. Those that did existed all depended on batteries and were only reserved for special occasions.
People, or animals, who managed to find their way in and were affiliated with the Outside's political forces disappear, never to be heard from again. The name, Hidden Continents, came to life. Unplottable, untraceable, none succeeded in contacting the Hidden Shinobi Nations. No wizard since Wizarding Year 1541, ever saw a ninja. They only existed inside ancient historical documents. To us these days, ninjas are a fairy tale. A child's bedtime story, if you will...
- Advanced History of Magic, Bathilda Bagshot