In May 2000, a new affair stirred up the foundations of the whole country. The affair was exposed in an investigative report published by the journalists Anat Tal - Shir and Zadock Yechezkeli in the weekend section "7 days" of 'Yediot Achronot'.

The article revealed that dozens of naval commando fighters have been afflicted with cancer after conducting regular diving training sessions in the Kishon as part of their regular training. The article revealed that at least 20 soldiers have been afflicted with cancer after years of diving in the Kishon and some of them have already died of cancer. The main protagonist of the journalistic coverage was Yuval Tamir who was afflicted with colon and skin cancer. More naval commando soldiers who also suffer from all kind of cancer interviewed along with him. The main claim of Tamir centered on the nonrecognition by the military system of its responsibility for his disease and thus, its unwillingness to participate in the high medical cost.

The media exposure brought about unprecedented public attention to environmental issues. The Chief of Staff appointed in July 2000, a commission of inquiry to evaluate the implications on the military activity in the Kishon river and the effect of the water in the region on the health of the soldiers who trained in the area. In fact, the goal of the inquiry commission was to determine if there was a connection between diving in the Kishon and the cancer contracted by the soldiers. The commission was headed by the retired judge, Meir Shamgar, the ex - chief justice, ex - Attorney General and one of the highest moral and legal authority in Israel. The commission also included Prof. Meir Vilchek, a renowned chemist of the Technion and Dr. Gabi Renrat, an expert on cancer of Carmel Hospital in Haifa.

Following three years of extensive hearings, testimonies, medical examinations and complicated statistical analysis, the commission held that there is not a distinctive connection between diving in the Kishon and the cancer contracted by the naval soldiers. The decision was made with a majority of two against one, when Judge Shamgar was of the minority opinion holding that there is a reasonable and casual connection between the condition of the Kishon during the relevant period and the cancer. The decision was received with shock by the naval commando fighters and other public bodies and elicited wide public echo. About a week after the conclusions were published, Shaul Mofaz, the ex - Lieutenant General, the minister of defense, announced that he adopts the dissenting opinion of judge Shamgar and thus, in fact, rejected the official conclusions of the commission and instructed the ministry of defense to compensate the soldiers.  

Since the journalistic revelation, the story received the name "the Kishon Affair" and is, still today, an inseparable part of the public/environmental talk. In special interview for the 55 year celebrations of the establishment of the state of Israel, Lieutenant General Bugi Yaalon, the current Chief of Staff, was asked about the "Kishon Affair." In his response, he said, "in the commission there were experts that regardless of their reservations, recommended unanimously to legally recognize the heavy divers who dived in the Kishon since it was polluted as casualties of the defense system. The controversy applies only to other divers if they should be recognized indulgently or legally, but in any case, the decision of the defense minister to recognize everyone by law is significantly valuable." Another updated example is the public discussion that is taking place in recent days dealing with the army plans to build the "city for training center" in the south, near Ramat Hovav. When an anonymous source in the environment office was asked to clarify the extent of risk in such plans, he was quoted in the media saying, "the Kishon Affair would seem as a child play compared with the disaster waiting to happen to soldiers who will serve in the targeted site."