Considering ninja first arrived on the scene in the 15th and 16th centuries, Japan seems to have taken a long time to get around to establishing a 'Ninja Council.' According to the Japan Times, a Ninja Council has now officially been formed across the country - although probably not for the reasons you'd thought... or hoped.
You see, this Ninja Council hasn't been established to cause international crises through the shady assassination of selected heads of state, neither has it been formed to wipe out global super-criminals which no other state agency can handle. Instead, it's been created to promote tourism, which - let's face it - isn't as exciting as you'd hoped.
A group of Japanese mayors and regional governors have come together to take advantage of the global pop-culture interest surrounding ninja. They even went so far as ditch their office attire in favor of the black garb of the famous assassins - although they didn't manage to look quite as fearsome.
Hiroshi Mizohata, former head of Japan's Tourism Agency, claimed ninja are frequently mentioned to him on his trips abroad, which led him to decide to put the masters of stealth front and center. Thankfully, the report recognized the irony of this move, and states this was a location ninja would historically try to avoid.
Eikei Suzuki, the governor of Mie prefecture, hoped the rise in interest of ninja could help revitalize Japanese communities, especially those in his region. The prefecture of Mie, especially the city of Iga, is often claimed to be the birthplace of ninjitsu - the martial art discipline of the ninja. The Mie University even offers a course in ninja studies, including lessons on walking stealthily and breathing methods to prevent fatigue.
However, historians interested in ninja - or shinobi as they're more commonly known - will probably end up frustrated by this advertising campaign. Modern depictions of ninja are not exactly the most historically accurate, and almost all derive from the Meiji Restoration period. During this time in the 19th century, ninja became major elements in folklore and imagination in Japan, with the fact slowly being overwritten by fantasy.
In fact, ninja probably hardly ever wore the black robes we often see them in today, instead favoring inconspicuous civilian clothing. Furthermore, they would also try to avoid combat if possible, more frequently being used for espionage, sabotage and reconnaissance.