A ministry spokesman said that the Namibian delegation accompanying President Hifikepunye Pohamba on a visit to Berlin said they needed to consult further with officials at home before signing the agreement.
"I regret this," said German minister for development and cooperation Heidemarie Wieczorek-Zeul.
"This was unexpected for us because the text had been agreed beforehand," the spokesman said.
The reparations Germany is offering amount to 20 million euros ($23.6 million) over a 10-year period beginning in 2006.
Wieczorek-Zeul expressed last year Germany's regret for the Herero and Dama deaths, during an event marking the centenary of the massacre.
Defending land expropriation
After meeting new German Chancellor Angela Merkel on Monday, Pohamba defended his government's policy of expropriating white-owned farms in the southern African state.
"Our new constitutions allow the expropriation of land by the government in the interests of the public."
Pohamba said the government amended the constitution after it realised that buying land from farmers for the landless on a "willing seller, willing buyer" basis, a policy adopted in 1991, "was not working at the pace we wanted".
The expropriation policy has caused controversy in Germany as some of the farmers who have been forced to leave their land were German citizens.