Morgan, a former New Zealand First MP, beat George Ngatai of Auckland for the job.
Incumbent Naida Glavish withdrew her nomination.
Morgan has been a member of the party for many years but has been active only in the past year or two.
He is the representative of King Tuheitia on Te Arataura, Waikato-Tainui's executive organisation.
While the Kingitanga itself is apolitical, it has been linked more closely with Labour through association. Labour's longest serving MP, Nanaia Mahuta, is a niece of the late Queen Dame Te Atairangikaahu and a cousin of King Tuheitia.
The AGM was held at Te Manukanuka o Hoturoa Marae, near Auckland Airport.