Leakey proposed controversial interpretations of his fossil finds. In two books written with science writer Roger Lewin, Origins (1977) and People of the Lake (1978), Leakey presented his view that, some 3 million years ago, three hominin forms coexisted: Homo habilis, Australopithecus africanus (Australopithecus), and Australopithecus boisei. He argued that the two australopith forms eventually died out and that H. habilis evolved into Homo erectus, the direct ancestor of Homo sapiens, or modern human beings. He claimed to have found evidence at Koobi Fora to support this theory. Of particular importance is an almost completely reconstructed fossil skull found in more than 300 fragments in 1972 (coded as KNM-ER 1470). Leakey believed that the skull represented H. habilis and that this relatively large-brained, upright, bipedal form of Homo lived in eastern Africa as early as 2.5 million or even 3.5 million years ago. Further elaboration of Leakey's views was given in his work The Making of Mankind (1981).

From 1968 to 1989 Leakey was director of the National Museums of Kenya. In 1989 he was made director of the Wildlife Conservation and Management Department (the precursor to the Kenya Wildlife Service 【KWS】). Devoted to the preservation of Kenya's wildlife and sanctuaries, he embarked on a campaign to reduce corruption within the KWS, crack down (often using force) on ivory poachers, and restore the security of Kenya's national parks. In doing so he made numerous enemies. In 1993 he survived a plane crash in which he lost both his legs below the knee. The following year he resigned his post at the KWS, citing interference by Kenyan President Daniel arap Moi (Moi, Daniel arap)'s government, and became a founding member of the opposition political party Safina (Swahili for “Noah's ark”). Pressure by foreign donors led to Leakey's brief return to the KWS (1998–99) and to a short stint as secretary to the cabinet (1999–2001). Thereafter he dedicated himself to lecturing and writing on the conservation of wildlife and the environment. Another book with Roger Lewin was The Sixth Extinction: Patterns of Life and the Future of Humankind (1995), in which he argued that human beings have been responsible for a catastrophic reduction in the number of plant and animal species living on the Earth. Leakey later collaborated with Virginia Morell to write his second memoir, Wildlife Wars: My Fight to Save Africa's Natural Treasures (2001; his first memoir, One Life, was written in 1983). In 2004 Leakey founded WildlifeDirect, an Internet-based nonprofit conservation organization designed to disseminate information about endangered species and to connect donors to conservation efforts. He also served in 2007 as interim chair of the Kenya branch of Transparency International, a global coalition against corruption.

Leakey's wife, zoologist Meave Leakey (Leakey, Meave G.) (née Epps), conducted numerous paleoanthropological projects in the Turkana region, often in collaboration with their daughter Louise (b. 1972). In 1998 her team discovered fossil remains, more than three million years old, of a hominin that she named Kenyanthropus platyops.