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.
The organs will be removed later in the day, according to the JOTN.
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.
The government's action followed revelations over the past 6 months that the JOTN had been involved in funneling the money since 1995 from the JOTN and the Japan Owners' Association (JOA), Japan's leading organization of horse owners, which coincidentally was also headed by Komurasaki.
*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.
He claims in the lawsuit that the article is unfounded and gave readers the impression he misappropriated the association's funds and bought the support of senior members of the JOTN
As JOA head, Komurasaki, 74, arranged donations totaling 800 million yen to the JOTN and a number of related medical facilities from 1995 to April last year, sources close to him said earlier.
But the panel consisted of JOTN President Eiichi Kakei and professors working for various transplant facilities.
The JOTN, a non-profit organization which coordinates organ transplants in Japan, also hired a freelance writer, who is an acquaintance of JOTN executive director Tatsuro Mori, as editor of the JOTN quarterly, Transplant, and paid her 7.5 million yen a year, the sources said.
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.