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In November, 1999, the Kenyan government tried to deport Kaiser, claiming that his work permit had expired.Kaiser briefly went into hiding in Kisii before he was granted a new work permit, but only after intervention by the US Ambassador Johnnie Carson and Bishop Colin Davis of Ngong.

In March, 2000, the independent Law Society of Kenya presented Kaiser with its annual Human Rights Award, for his public testimony before the Akiwumi Commission and his support of the two girls. They called him "a study in courage, determination and sacrifice on behalf of the weak, oppressed and downtrodden."
Kaiser knew of the dangers of speaking out in Kenya, and of a fate which had befallen many others. In a book about his experiences at the Maela camp, he wrote a warning.

"I want all to know that if I disappear from the scene, because the bush is vast and hyenas many, that I am not planning any accident, nor, God forbid, any self destruction. Instead, I trust in a good guardian angel and in the action of grace.If I Die," John Kaiser


On August 23, 2000, Kaiser was shot in the back of the head with a shotgun, at close range. His body was found at 6 am the next day beneath two acacia trees by a butcher named George, at Morendat junction on the Nakuru-Naivasha road in western Kenya. He was carrying documents he intended to present to the Akiwumi Commission. He was also to testify against the Moi government before the International Criminal Court in the Hague in three weeks.The first police officers on the scene thought he had been murdered.

Less than a week after Kaiser's death, Florence Mpayei dropped her rape case against Julius Sunkuli.

Kenya's chief government pathologist and a pathologist from an independent human rights organization present at the autopsy thought Kaiser was killed from a muzzle distance of about 3 feet (0.91 m), from which suicide would be impossible. However, an FBI expert from Texas, who did not examine Kaiser but only saw photographs, concluded that Kaiser had committed suicide. The Moi government readily agreed.

Both houses of the United States Congress passed a joint resolution calling Kaiser's death "an assassination", and calling for the US State Department to investigate.