"We are working towards a joint government declaration with the following elements: common discussions on the historical events and a German apology for the action in Namibia," the spokeswoman, Sawsan Chebli, told reporters.
The joint declaration with the Namibian government can serve as a basis for a parliamentary resolution, she said, adding however that the step would not translate into legal repercussions for Germany.
"On the question of whether there could be reparations or legal consequences, there are none. The apology does not come with any consequences on how we deal with the history and portray it," she said.
Berlin ruled what was then called South-West Africa as a colony from 1884 to 1915.
Incensed by German settlers stealing their land and cattle and taking their women, the Herero people launched a revolt in January 1904 with warriors butchering 123 German civilians over several days. The Nama tribe joined the uprising in 1905.
The colonial rulers responded ruthlessly and General Lothar von Trotha signed a notorious extermination order against the Hereros.
Rounded up in prison camps, captured Namas and Hereros died from malnutrition and severe weather. Dozens were beheaded after their deaths and their skulls sent to German researchers in Berlin for "scientific" experiments.
Up to 80,000 Hereros lived in Namibia when the uprising began. Afterwards, only 15,000 were left.
Germany has since 2011 formally handed back dozens of the skulls.
But Berlin has repeatedly refused to pay reparations, saying that its hundreds of millions of euros in development aid since Namibia's independence from South Africa in 1990 was "for the benefit of all Namibians".
The speaker of the German parliament last July said the slaughter of indigenous Namibians a century ago constituted a "genocide" that stemmed from a "race war".
Norbert Lammert, writing in a guest column for news weekly Die Zeit, said the Herero and Nama peoples had been systematically targeted for massacre by German imperial troops.
Since then, the government has also used the term, with Chebli on Wednesday also saying that "we have spoken of genocide for a long time."
German lawmakers in June passed a resolution recognising the World War I massacre of Armenians by Ottoman forces as genocide, drawing a furious rebuke from Turkey which called it a "historic mistake".