A further six Maori remains being returned were either collected or traded by Henry Suter, an early Swiss settler who arrived in New Zealand in 1887.
Three of the skeletal remains had connections to Whangaroa in Northland. Other remains had connections to Tainui and elsewhere in New Zealand.
Ubersee Museum director Wiebke Ahrndt said there was no ethical reason to justify the bones remaining in Bremen.
"The provenance research undertaken has been able to shed light on the circumstances under which this collection was acquired. It also made clear that there is no longer any ethical justification for retaining the ancestral remains of the Moriori and Maori in our collections."
Bremen's Mayor Carsten Sieling apologised for the actions of the collectors and traders during the colonial age saying collecting the bones contravened human dignity. He asked for forgiveness and was pleased the ancestral remains could return home.
Te Papa kaihautu (leader) Dr Arapata Hakiwai praised the work of the Bremen museum but said the repatriation highlighted the lack of respect shown to wahi tapu by early settlers.
The museum would now be working to return the bones to iwi.
The remains are part of 59 ancestral remains returning from four institutions in Europe. Bones from Sweden are already on their way.
The bones will be formally welcomed back on May 26 with a powhiri at Te Papa.