The bodies of the women, aged 28 and 47, were discovered at the Fish River Canyon, Africa's largest canyon, in the south of the country.
Police spokesman Slogan Matheus told AFP in a statement that the pair had come to Namibia to collect the remains of a family member who had died last month in the former German colony.
But he declined to give further details about the women, saying the families had not yet been formally notified.
Matheus said the police were notified on Saturday that two German visitors who went hiking on Thursday had not returned.
"Today (Monday) at about 10:50 am (0850 GMT), the police found the bodies of the two missing German tourists at the Fish River Canyon," police said.
An investigation has been launched into the circumstances of their deaths.
Namibian police chief Sebastian Ndeitunga told AFP that he had been told by his officials that the two may have planned to commit suicide in Namibia.
He said he would be "disappointed if the allegations that the two tourists came to commit suicide here are true. This is a rare case," said Ndeitunga.
"We can't confirm that because the deceased left quite a few of their documents, and we can't at this stage interpret any to be a suicide note," Matheus told AFP.
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