The Konoha shinobi society is organised into several units placed under the control of the Hokage. Each unit has Jōnin or Special (Tokubetsu) Jōnin in charge of it, and they report to the Hokage and his advisers.

The Hokage sits at the top of the society, discussing issues with their Advisors. The two official advisers of Hiruzen Sarutobi are Mitokado Homura, and Utatane Koharu, living through the previous wars together.

The Jōnin Commander supports the Hokage, aiding in directing the villages units and representing the regular forces.

Some groups and units known only the the Hokage and higher ranking individuals. ROOT was one of these secretive organisations, a sub-division of the ANBU initially shut down by the Sandaime, illegally operated until it was finally disbanded after Danzo Shimura’s death during the Godaime reign.

Operations Unit:

In other words, regular shinobi forces which are the backbone of the system. Teams or specific individuals handle the majority of the missions that the village receives, and are also tasked with other duties such as education, administration, etc. Most ninja are in this division, from genin, chūnin, special jōnin and jōnin.

Medical Corps:

The medical teams and medical-nin within this sector support the general shinobi forces through healing the sick and injured whether in village (coordinating with ordinary doctors) or on the battle field. They develop new techniques, study medicines, research diseases and further their anatomy understanding to advance their healing capabilities. They are divided into several groups by speciality, such as emergency staff or technical research. Some medical-nin are skilled enough to join regular forces and are called field medical-nin.

ANBU:

This division is under direct control of the Hokage, and only accept order from them. They are covert operatives who specialise in spying, assassination, and other difficult or risky missions. The Hokage selects them personally, regardless of age or gender, and they are meant to be the most elite of the forces. The individual units are composed according to the goal and difficulty of their missions.

Konoha Intelligence Division:

This organisation within the village is composed of many sub-divisions, such as the Konoha Torture and Interrogation Force which is a special division headed by Ibiki Morino. Prior to the fourth shinobi war, they worked alongside the Analysis Team which was headed by Inoichi Yamanaka. Prisoners or the dead are kept here here to extract information from them for the benefit of Konoha.

- Chūbu appears to be a modern ranking in Konoha given to Sai, and implies it may be a type of support unit.

- The Twenty Platoons (Nijū Shōtai) were created by the Godaime, Tsunade Senju, to search for the Akatsuki. It consisted of twenty teams of four individuals.

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Outside of Konoha, other lands follow their own customs and culture which creates a different type of organisation within the individual villages.

*Shinobi Ruler/Head Shinobi - A rank found within Kumo above jonin, they’re given the authority to represent their village’s interests.

*Kinkaku Force was an elite team of twenty shinobi from Kumo, which is now disbanded.

*Hunter Squads - A special unit of Kiri’s own Hunter-nin, created solely to hunt down and dispose of rogue shinobi/missing-nin, they possess medical and assassination training to aid their goals.

*Twelve Guardian Ninja are a group of twelve elite shinobi invited by the Land of Fire’s Daimyo to become his body guards.

*Puppet Brigade was a division in Suna of skilled puppeteers during the Second Shinobi War.

*Explosion Corps was an organisation within Iwa composed of individuals holding the explosion release kekkei genkai.

*Seven Ninja Swordsmen of the Mist is an organisation of seven skilled individuals who wielded the legendary blades of Kiri.