A Namibian government delegation will receive the remains, including 19 skulls, a scalp and bones, during a solemn church service in Berlin.
“We want to help heal the wounds from the atrocities committed by Germans at the time,” said Michelle Muentefering, a minister of state for international cultural policies in the German foreign ministry.
But representatives of descendants of the tens of thousands of Herero and Nama people massacred between 1904 and 1908 after rebelling against their colonial overlords have criticised the ceremony as insufficient.
Esther Utjiua Muinjangue, chairwoman of the Ovaherero Genocide Foundation, said the handover would have been “the perfect opportunity” for Germany to officially apologise for what is often called the first genocide of the 20th century.
“Is that asking too much? I don't think so,” she told a Berlin press conference this week, describing the attitude of the German government as “shocking”.
State Minister Muentefering told reporters on Monday that Germany still has “a lot of catching up to do in coming to terms with our colonial heritage”.
As part of ongoing talks with the Namibian government on addressing its brutal legacy in what was then South West Africa, the German government said in 2016 that it planned to issue a formal apology.
But the negotiations aimed at coming up with a joint declaration on the massacres are still ongoing.
Although Berlin has acknowledged the horrors that occurred at the hands of German imperial troops, it has refused to pay direct reparations.
It has argued instead that German development aid worth hundreds of millions of euros since Namibia's independence from South Africa in 1990 was “for the benefit of all Namibians”.
Angered by Berlin's stance, representatives of the Herero and Nama people have filed a class-action lawsuit in a US court demanding reparations.
They also want to be included in the discussions between Germany and Namibia.
Germany wants the lawsuit thrown out on the grounds of state immunity for prosecution.
The New York judge in the case has yet to rule on whether to hear the lawsuit.
Namibian Culture Minister Katrina Hanse-Himarwa, speaking alongside Muentefering in Berlin, said the two countries “still have many problems to solve”.
“We must ensure that after we've reached agreements on damages, recognition and an apology, there's a future in which the German and Namibian nations join hands and move forward.”
Incensed by German settlers stealing their land, women and cattle, the Hereros revolted in 1904 and killed more than 100 German civilians over several days. The Nama people joined the uprising in 1905.
Determined to crush the rebellion, General Lothar von Trotha signed a notorious “extermination order” that would lead to the deaths of some 60,000 Hereros and 10,000 Nama people.
Many were murdered by German imperial troops while others, rounded up in prison camps, died from hunger and exposure.
Dozens were beheaded after their deaths, their skulls sent to researchers in Germany for discredited “scientific” experiments that purported to prove the racial superiority of white Europeans.
In some instances, captured Herero women were made to boil the decapitated heads and scrape them clean with shards of glass.
Research carried out by German professor Eugen Fischer on the skulls and bones resulted in theories later used by the Nazis to justify the murder of Jews.
Wednesday's handover proceedings mark the third time that Germany has repatriated human remains to Namibia, the previous occasions were in 2011 and 2014.
The remains, many of which were stored on dusty shelves in universities and clinics, were “often stolen… brought to Germany without respect for human dignity”, according to the German foreign ministry.
Herero activist Muinjangue said the homecoming of the bones was always “very emotional”.
“I'm looking at the skull of a Herero or Nama peasant. A peasant who could have been my great-grandmother or great-great grandmother or father.”