Mana Motuhake was formed by in 1979 by Matiu Rata, a member of the Labour Party. Rata had served as Minister of Māori Affairs in the third Labour government (1972 - 1975), but grew increasingly dissatisfied with the party's policy. Eventually deciding that Māori needed an independent voice, he quit the Labour Party in 1979. Shortly afterwards, he founded Mana Motuhake, and resigned from Parliament to contest a by-election under its banner. In the Northern Māori by-election of 1980, however, Rata was narrowly defeated by the new Labour candidate, Bruce Gregory.
Mana Motuhake stood candidates in the 1981 elections, 1984 elections, 1987 elections, and 1990 elections, but was unsuccessful on each occasion. In 1991, the party agreed to join forces with three other political parties (NewLabour Party, the Green Party, and the Democratic Party) to form a single group, known as the Alliance. This decision was controversial, as a number of prominent figures in Mana Motuhake believed that by joining the party with non-Māori parties, even sympathetic ones, the party would no longer be free to speak up for Maori. Those who supported the continuation of an independent Māori party founded the new Mana Māori party, led by Eva Rickard.
In the 1993 elections, a Mana Motuhake candidate, Sandra Lee-Vercoe, was elected to Parliament under the Alliance banner. When Rata retired the following year, Lee-Vercoe became Mana Motuhake's political leader. With the introduction of the MMP electoral system in the 1996 elections, Lee-Vercoe was joined in Parliament by Alamein Kopu. Kopu, however, eventually left the party, founding her own Mana Wahine Te Ira Tangata party. In the 1999 elections, another Mana Motuhake candidate, Willie Jackson, entered Parliament as an Alliance MP. In 2001, Jackson successfully challenged Lee-Vercoe for leadership of the party.
In 2002, when the Alliance split into moderate and radical factions, Mana Motuhake sided with the radicals, led by Laila Harré and Matt McCarten. Lee-Vercoe, the former leader, sided with Jim Anderton's moderate faction, but decided to retire from Parliament rather than stand for his breakaway Progressive Party. In the 2002 elections, the remnants of the Alliance were defeated, and Mana Motuhake was left without representation in Parliament. Shortly afterwards, it left the Alliance.