Yakukin were provided to those who were in certain posts such as ongoku bugyo (magistrates assigned to key domains under the direct control of the bakufu), in addition to the executive allowances called yakuryo. It is also said the yakukin is a substitute for yakuryo, but yakukin is now regarded as another allowance deriving from a different system since yakukin was paid together with yakuryo in some cases. Yakukin was paid mainly to officers working in provincial areas, including high-ranking bugyo and middle-ranking kumigashira. According to "Richo" (a book on office organizations in the Edo bakufu), 30,000 ryo was paid to Nagasaki bugyo, 100 ryo to each bugyo shihai kumigashira (officers supporting bugyo) in Nagasaki, Uraga and Sado, 70 ryo to those in Niigata, 80 ryo to tsutsumi bugyo (magistrate in charge of river banks) concurrently working as kaisen aratameyaku (supervisor in charge of cargo vessels) in Sekka Shu (Kawachi Province), 25 ryo to gonyuyo torishirabeyaku (auditor for the Kyoto Imperial Palace) in Kyoto, 10 ryo to bugyo shihai ginmiyaku (officers supporting bugyo) in Nikko, and 20 ryo each to ozendokoro kumigashira (head of the food department) and okuozendokoro kumigashira (head of the inner palace food department).
On October 23, 1867, the Edo bakufu made reform by introducing a system to collect a half of the territory revenue instead of the abolished military service system applied to hatamoto (direct retainers of the bakufu) and gokenin (vassals) while integrating yakuryo, tashidaka (supplementary stipends), yakuryo and yakubuchi (monthly salaries) paid to those who were in hoi and higher positions (from Jushiinojo [Junior Fourth Rank, Upper Grade] Upper Grade) to Jugoinoge [Junior Fifth Rank, Lower Grade]) into yakikin. Typical yakukin were 10,000 ryo paid to roju (members of the shogun's council of elders), 5,000 ryo to the posts equal to roju, 4,000 ryo to wakadoshiyori (the position next to roju) and sobayonin (political coordinators), and 2,500 ryo to rusui (officer in charge of the Inner Palace), rikugun bugyo nami (deputy magistrate in charge of army), kaigun bugyo nami (deputy magistrate in charge of navy), gaikoku sobugyo nami (deputy general magistrate in charge of foreign affairs), ometsuke (chief inspector of the Edo shogunate), machi bugyo (magistrate in charge of administration of Edo), and kanjo bugyo (commissioner of finance) (however, these amounts were restricted according to stipends of the territory). The collection of military service fees and payment of yakukin allowances was to be done quarterly (in March, June, September and December), but this system ended without functioning in full due to the Taisei Hokan (transfer of power back to the Emperor) implemented in the following month.
However, in some cases, the word "yakukin" was used in different meanings from the above: for example, salaries paid to village and town representatives, impositions on bankers, and impositions on pond fishers as "pond fishing charges."