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.
"Using today's standards of international law, the crushing of the Herero revolt was genocide," he wrote.
Lammert said Germany had perpetrated a "race war" in Namibia.
"There were tens of thousands of Herero and Nama victims, not only through fighting but also illness and the targeted killing through allowing people to die of thirst and hunger," he said.
"Others died in concentration camps and in slave labour."
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, many of which were stored on dusty shelves at universities and clinics.
But it 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".
Ahead of the centenary of the end of German rule in Namibia, activist groups and opposition parties have resumed calls for a cash settlement and a formal acknowledgement from Berlin of a genocide.
In April, President Joachim Gauck joined Lammert in for the first time calling the slaughter of an estimated 1.5 million Armenians by Ottoman forces in 1915 a "genocide".
But Foreign Minister Frank-Walter Steinmeier said he would not adopt the label, arguing it could play into the hands of those who sought to minimise the singular horror of the Holocaust, in which Nazi Germany killed six million European Jews.