The Waitangi National Trust was set up to administer the estate.
The bill removes a potential conflict between the constitutional and trusteeship roles of the Governor-General and Government ministers who are also members of the board by providing fixed terms of appointment for board members.
Other members of the board include representatives of some of the nation's most significant historical figures including Hone Heke, Maihi Kawiti, Tamati Waka Nene, James Busby, Archdeacon Henry Williams and Edward Gibbon Wakefield.
Under changes to be made by the bill, the Governor-General will become the trust's honorary patron, while two Members of Parliament will be appointed as full members of the board - one by the Prime Minister and one by the leader of the opposition.
Previously, the Governor-General and ministers were listed in the Act as members of the board. The amendments separate the roles of trustees and the constitutional roles of ministers.
Treaty Negotiations Minister Christopher Finlayson said the bill was timely with the 175th anniversary of the signing of the Treaty next year.
The bill passed its first reading unanimously, and will now be considered by the Maori Affairs select committee.