JOTN, headed by Yoshio Komurasaki, allegedly acted as a go-between in funneling millions of yen in company donations to various societies and organizations, receiving 5% each time in commission.
The health ministry told the JOTN not to accept donations as a public entity.
Under the plan, the senior managing director will repay 15% of his salary and a pay hike for JOTN employees will be suspended.
Under the JOTN
's selection procedures, organ recipients are chosen from among those registered with the JOTN
based on the urgency of their medical conditions.
As JOA head, Komurasaki arranged donations totaling $800 million yen to the JOTN and a number of related medical facilities from 1995 to April last year.
The JOA allegedly funneled 70 million yen to the former chiefs of two panels under the predecessor of the Health, Labor and Welfare Ministry before the JOTN was established in October of 1997.
The JOTN funneled 75 million yen in corporate donations in 1997 and 1998 so that the donating companies could get preferential tax treatment.
But the panel consisted of JOTN President Eiichi Kakei and professors working for various transplant facilities.
On Wednesday, Komurasaki's replacement Yuzo Tanimizu told reporters it is difficult to identify all receivers of donations from the JOA and to figure out relations between them and the JOTN.
Another allegation is about the JOA's and the health ministry's involvement in setting up the JOTN.
A JOTN board member said the JOTN budget is tight because of cuts in government subsidies and non-profit organizations should hold public bidding before awarding contracts.
The Health, Labor and Welfare Ministry plans to conduct an on-site inspection at the JOTN office Wednesday to ascertain how the contracts were made with companies owned by relatives of JOTN executives.