In addition to conducting archaeological investigations, Leakey headed the National Museums of Kenya (1974-89) and the Department of Archaeological Sites. An outspoken advocate of wildlife conservation, he helped to promote a worldwide ban on the ivory trade and in 1989 became the director of the Kenya Wildlife Service, He overhauled the agency, but in 1994 he broke with Kenyan president Daniel arap Moi and resigned.

In 1995 he joined other opponents of Moi's government in forming the prodemocracy, anticorruption Safina [Ark] party, and he was elected to parliament (1997) as a member of the opposition. He was reconciled with Moi in 1998 and again became head of the wildlife service. In 1999 he was named head of the Kenyan civil service, but he resigned in 2001. He has since co-founded WildlifeDirect.org, an online network launched in 2006 that enables African conservationists and wildlife parks and reserves to reach donors and other supporters worldwide.

Leakey's second wife, Meave G. Leakey, a paleontologist, discovered (1996) the remains of the 4-million-year-old Australopithecus anamensis. In 2001 a team she headed argued that a 3.5-million-year-old skull unearthed in Kenya represented a hominid genus and species, Kenyanthropus platyops, distinct from the contemporary Australopithecus afarensis.