They have been highly prized by collectors in North American, Europe and Australia.
Te Papa acting chief executive and kaihautu Arapata Hakiwai said there was an encouraging shift in the attitudes among overseas institutions about the repatriation of ancestral remains.
"Slowly and gradually our ancestors are returning home, with the genuine well wishes of the museums and institutions where they have been housed for a number of years."
Milwaukee Public Museum president and chief executive Dennis Kois said they were proud to assist in the journey of a tupuna, or ancestor, back to its homeland in New Zealand.
"Out of respect for Maori and their customs, the museum's board of directors, as well as the Milwaukee County Board, approved the deaccessioning and return of the ancestor."
After returning to New Zealand, the toi moko will be placed in Te Papa's Wahi Tapu, or sacred repository, where it will be cared for until further research reveals its tribe of origin.