JETs are not employed directly by the national Japanese government, "the JET Programme" or CLAIR. Each JET Programme participant signs their employment contract with an individual contracting organisation or CO.
- For ALTs, COs can be prefectural/designated city boards of education, municipal (city/town/village) boards of education or individual private schools.
- For CIRs and SEAs, COs can be the prefectural/designated city government, a municipal (city/town/village) government or a related organisation.
Although each contracting organisation bases their employment contract on the model JET contract, the actual terms can and do vary between COs. This results in disparities between JETs and is a frequent source of resentment for many. Differences can include amount of nenkyu allocated, daikyu availability and the conditions under which these can be taken.
Aside from written differences in JET's contracts, their interpretation also varies widely between COs. Some COs require their ALTs to come into the office during school holidays, while others do not; some COs subsidise rent, while others do not. Each JET's individual relationship with their supervisor can often be the determining factor in how they are treated.