Era of shoguns and samurai is long over, but Japan does have one, or maybe two, surviving ninjas.

Experts in the dark arts of espionage and silent assassination, ninjas passed skills from father to son – but today’s say they will be the last.

Japan’s ninjas were all about mystery. Hired by noble samurai warriors to spy, sabotage and kill, their dark outfits usually covered everything but their eyes, leaving them virtually invisible in shadow – until they struck.

Using weapons such as shuriken, a sharpened star-shaped projectile, and the fukiya blowpipe, they were silent but deadly.

Ninjas were also famed swordsmen. They used their weapons not just to kill but to help them climb stone walls, to sneak into a castle or observe their enemies.

Most of their missions were secret so there are very few official documents detailing their activities. Their tools and methods were passed down for generations by word of mouth.

This has allowed filmmakers, novelists and comic artists to use their wild imagination.

Hollywood movies such as Enter the Ninja and American Ninja portray them as superhumans who could run on water or disappear in the blink of an eye.

“That is impossible because no matter how much you train, ninjas were people,” laughs Jinichi Kawakami, Japan’s last ninja grandmaster, according to the Iga-ryu ninja museum.

However, ninjas did apparently have floats that enabled them move across water in a standing position.

Kawakami is the 21st head of the Ban family, one of 53 that made up the Koka ninja clan. He started learning ninjutsu (ninja techniques) when he was six, from his master, Masazo Ishida.

“I thought we were just playing and didn’t think I was learning ninjutsu,” he says.

“I even wondered if he was training me to be a thief because he taught me how to walk quietly and how to break into a house.”

Era of shoguns and samurai is long over, but Japan does have one, or maybe two, surviving ninjas

Other skills that he mastered include making explosives and mixing medicines.

“I can still mix some herbs to create poison which doesn’t necessarily kill but can make one believe that they have a contagious disease,” he says.

Kawakami inherited the clan’s ancient scrolls when he was 18.

While it was common for these skills to be passed down from father to son, many young men were also adopted into the ninja clans.

There were at least 49 of these but Jinichi Kawakami’s Koka clan and the neighboring Iga clan remain two of the most famous thanks to their work for powerful feudal lords such as Ieyasu Tokugawa – who united Japan after centuries of civil wars when he won the Battle of Sekigahara in 1600.

It is during the Tokugawa era – known as Edo – when official documents make brief references to ninjas’ activities.

“They weren’t just killers like some people believe from the movies,” says Jinichi Kawakami.

In fact, they had day jobs. “Because you cannot make a living being a ninja,” he laughs.

There are many theories about these day jobs. Some ninjas are believed to have been farmers, and others pedlars who used their day jobs to spy.

“We believe some became samurai during the Edo period,” says Jinichi Kawakami.

“They had to be categorized under the four caste classes set by the Tokugawa government: warrior, farmers, artisan and merchants.”

As for the 21st Century ninja, Kawakami is a trained engineer. In his suit, he looks like any other Japanese businessman.

The title of “Japan’s last ninja”, however, may not be his alone. Eighty-year-old Masaaki Hatsumi says he is the leader of another surviving ninja clan – the Togakure clan.

Hatsumi is the founder of an international martial arts organization called Bujinkan, with more than 300,000 trainees worldwide.

“They include military and police personnel abroad,” he tells me at one of his training halls, known as dojo, in the town of Noda in Chiba prefecture.

It is a small town and not a place you would expect to see many foreigners. But the dojo, big enough for 48 tatami mats, is full of trainees who are glued to every move that Masaaki Hatsumi makes. His actions are not big, occasionally with some weapons, but mainly barehanded.

Masaaki Hatsumi explains to his pupils how those small moves can be used to take enemies out.

His reputation doesn’t stop there. He has contributed to countless films as a martial arts adviser, including the James Bond film You Only Live Twice, and continues to practice ninja techniques.

Both Kawakami and Masaaki Hatsumi are united on one point. Neither will appoint anyone to take over as the next ninja grandmaster.

“In the age of civil wars or during the Edo period, ninjas’ abilities to spy and kill, or mix medicine may have been useful,” Jinichi Kawakami says.

“But we now have guns, the internet and much better medicines, so the art of ninjutsu has no place in the modern age.”

As a result, he has decided not to take a protégé. He simply teaches ninja history part-time at Mie University.

Despite having so many pupils, Masaaki Hatsumi, too, has decided not to select an heir.

“My students will continue to practice some of the techniques that were used by ninjas, but [a person] must be destined to succeed the clan.” There is no such person, he says.

The ninjas will not be forgotten. But the once-feared secret assassins are now remembered chiefly through fictional characters in cartoons, movies and computer games, or as a tourist attractions.

The museum in the city of Iga welcomes visitors from across the world where a trained group, called Ashura, entertains them with an hourly performance of ninja tricks.

Unlike the silent art of ninjutsu, the shows that school children and foreign visitors watch today are loud and exciting. The mystery has gone even before the last ninja has died.