Although there are variations from village to village, the general organisational structure and hierarchy of the ninja systems of each village is about the same. At the top of the organisation is the village head, or the Kage in the case of the Five Great Shinobi Countries. They rule the village and its shinobi together with a council, usually consisting of highly ranked shinobi and elders.
The actual shinobi forces are divided in three groups. The regular forces, the Anbu, and the medical teams.
The regular forces (正規部隊, Seiki Butai) form the foundation of the village and its shinobi system. The majority of shinobi are a part of these forces and together, either individually or in teams, they perform the majority of the missions the village receives. They are also tasked with the various duties within the organisation, such as training and administrative duties.
When an Academy student graduates, they usually become a part of these forces, assuming the rank of genin. Via various exams and tests, they can be promoted to higher ranks, first to chūnin and jōnin after that. Sometimes, when a shinobi is specialised in a very specific skill, they can assume the rank of tokubetsu jōnin, which is a rank between chūnin and jōnin.
Main article: Academy Student Academy students (忍者学校生, Akademī-sei) make up the student body of the Academy, where they are trained and prepared for life as a shinobi. They are not an actual part of the shinobi force, as they are still in the process of mastering the very basics of the ninja lifestyle. However, they can be conscripted as part of the war potential in times of emergency.
Main article: Genin Genin (下忍; Literally meaning "low ninja", Meaning (Viz) "junior ninja") are the lowest level of ninja and also the ones that display the most difference in power. When they become genin, ninja start to do their bit for their village's economy – being sent on missions that the village gets paid for. They are typically sent either on D-rank missions, which are almost entirely risk-free jobs of manual labour, or, rarely, on C-rank missions, which are a cut above that and begin to verge on real "ninja" work that have a very low possibility of risk to the ninja involved. When Konohagakure was short-handed on upper-level ninja because of the invasion, the village had to occasionally send genin on higher-ranked missions.
Main article: Chūnin Chūnin (中忍; Literally meaning "Middle Ninja", Meaning (Viz) "Journeyman Ninja") are ninja who are qualified to guide other ninja and lead missions. Chūnin have reached a level of maturity and ability that primarily consists of leadership skills and tactical prowess. Genin who do not have the skills to become chūnin are weeded out in the chūnin exams. Some of them, like Iruka Umino, Daikoku Funeno and Suzume move on to function as Academy teachers and others, like Shikamaru Nara, serve as team leaders in charge of small teams who need to make decisions and utilise the skills of the shinobi under their command to the maximum effect. Chūnin are typically sent on C-rank or B-rank missions.
Main article: Tokubetsu Jōnin Tokubetsu Jōnin (特別上忍, Tokubetsu Jōnin; English TV "Special Jōnin"; Literally meaning "Special High Ninja"; sometimes known as Tokujō for short) are ninja who, rather than all-around jōnin training, have jōnin-level ability in a specific area or skill, much like warrant officers in real-world militaries. They are elite specialists in their areas and are often assigned as subordinates to regular jōnin when their services are needed.
Main article: Jōnin Jōnin (上忍, Jōnin; Literally meaning "High Ninja", Meaning (Viz) "Elite Ninja") are generally highly-experienced shinobi with great individual skill who serve as military captains. They are often sent on A-rank missions, and experienced jōnin may even be sent on S-rank missions (which are considered to be the greatest difficulty). It is not unusual for jōnin to go on missions alone. Jōnin are generally able to use at least two types of elemental chakra, proficient genjutsu, and decent taijutsu skills.
Main article: Kage A Kage (影; Literally meaning "Shadow") is the leader of one of the five most powerful hidden villages and are generally acknowledged as the most powerful ninja in their respective villages. They are collectively known as the Five Kage (五影, Gokage; Literally meaning "Five Shadows").
Although the higher-ranking members of the regular forces often perform missions alone, most are done in teams. The most basic team is the one a genin is placed in after graduation. This so-called three-man cell consists of three genin under the guidance of a jōnin commander. These teams are meant to give the new shinobi practical skills, while already being a productive member of the organisation. Usually, strong bonds are cultivated between the members of such a team, lasting their entire lives. Because of these bonds and the fact that working with one's long-time team-mates is usually more efficient, these teams often last even after all members have been promoted to chūnin or higher.
Besides these basic teams, there are also teams, and groups created for specific missions and tasks. Sometimes these are ad hoc teams which only exist for the duration of the mission, such as the Sasuke Retrieval Team, but in certain cases these teams are more organised and lasting, such as the Nijū Shōtai, created to battle the threat of Akatsuki.
Special Ranks and Functions
Besides the standard ranks of genin, chūnin, tokubetsu jōnin, and jōnin, there are some shinobi who bear a special rank or function. For instance, Kumogakure has a rank between that of jōnin and Raikage which is known as "Head Ninja". This person helps in leading the shinobi forces and is capable of representing the village officially. Konohagakure has the Jōnin Commander, who is selected from the jōnin population to represent the regular forces in council meetings and likely helps in commanding the regular forces.
Main article: Anbu The Anbu (暗部; English TV "Anbu Black Ops"; Literally meaning "Dark Side"), short for Ansatsu Senjutsu Tokushu Butai (暗殺戦術特殊部隊; Literally meaning "Special Assassination and Tactical Squad"), take orders directly from the Kage, performing special high-level missions, such as assassinations and torture. The Anbu usually work in teams formed to the requirements of the mission, ensuring maximum success. The shinobi in the Anbu are hand-picked by the Kage, chosen for their individual capabilities and special skills. Age, gender, background, or previous rank bear no weight in this decision. Members can be relieved from the Anbu by the Hokage and reassigned elsewhere, in Kakashi's case, he was reassigned by Hiruzen Sarutobi from the Anbu to the regular forces as a jōnin leader. They wear their mask even in their own village, for their identity as an Anbu agent is to be known only by the Kage and village elders, with the exception of Konohagakure's "Root" Anbu members who, unless ordered to, will only act on Danzō Shimura's orders.
There are apparently no true ranks within the Anbu, unlike within the regular forces. In Naruto 6: Road to Ninja, Sai told Naruto that Root members have their own ranking system different from the usual ninja, after the latter was complaining that he had no parents that would recommend him of being jōnin. Team leadership and hierarchy seem to be based on merit and experience. The leaders of the teams are called squad leaders (分隊長, Buntaichō), a position held in high regard.
There are various groups within the Anbu, aimed at various different functions and tasks. Kirigakure, for instance, has the hunter-nin — a group created solely for hunting down and disposing of missing-nin. Konohagakure has the ANBU Torture and Interrogation Force, who interrogate prisoners and work to gather intelligence. Though they were to officially disband, another Anbu faction named Root carried out extremely secretive missions and were not under the direct authority of previous Hokage.
The medical teams (医療班, Iryō-han) is the supporting side of the shinobi forces. They consist of medical-nin, working behind the scenes to heal sick and injured shinobi and to make sure the organisation's resources are always in peak condition. Medical-nin are similar to a Hospital Corpsman or HM of the military in real life. They also do extensive research into new techniques, medicines, diseases and the human body. Although not seen very often, they are highly respected. Even to a jōnin, the advanced skills of these shinobi seem like magic.
Not all medical-nin are members of the medical teams, though. There are also medical-nin within the regular forces, who go along on standard missions to increase the success-rate referred to as field medical-nin. Though medical-nin from the hospital are sent out into the fields from time to time as seen when a group of medical-nin were sent after the Sasuke Retrieval Team. However, back in the village, it is the medical teams who run the hospital and treat the wounded.