Waena was a Member of the National Parliament for Ulawa-Ugi constituency in the Makira-Ulawa Province from 1984 to 2004. He served as Deputy Speaker of Parliament before becoming Assistant Prime Minister and Minister of Provincial Government in 2000, and afterwards he became Minister for National Unity, Peace and Reconciliation.

He was elected as Governor-General by the National Parliament on June 15 2004. He received 27 of 41 votes, compared to 6 for incumbent Sir John Lapli and 8 for former Prime Minister Sir Peter Kenilorea.

Sir Nathaniel was knighted soon after assuming office and later awarded the Solomon Island Cross (CSI).

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