About schools and organizations teaching the art of Ninjutsu
One of the organizations generally accepted as teaching ninjutsu by the Bujinkan’s members is Bujinkan Doji which is headed by Masaaki Hatsumi. Only three of Hatsumi’s Bujinkan Dojo nine separate schools of traditional Japanese martial arts contain ninjutsu training. Toshitsugu Takamatsu taught Hatsumi a variety of martial arts, of which ninjutsu was just one.
The Genbukan headed by Shoto Tanemura and the Jinenkan headed by Fumio Manaka are two other modern organizations teaching ninjutsu. Both of these instructors have left the Bujinkan due to differences of teaching style but had achieved Menkyo Kaiden prior to leaving.
Other school may contain some aspects of ninjutsu but not be traditional ninjutsu schools. These include the traditional martial art of Tenshin Shoden Katori Shinto-ryu.
The traditional espionage techniques of ninjutsu are not usually a focus of ninjutsu in our modern era. They really no longer have a purpose and often only serve to attract students with unrealistic expectations and a lot of negative publicity for the art.