The Duke of Cambridge went rhino spotting with a team of local rangers on a 5 a.m. trek in the country's mountainous region, Kensington Palace said in a tweet.
He praised the "beauty and sheer remoteness" of Namibia's landscape as he spotted a rare black rhino after five hours.
The Duke of Cambridge said he was humbled by the rangers' dedication toward protecting Namibia's rhinos population from poachers.
"This why I wanted to come to Namibia — to listen and learn. It is also why Namibia's voice on these difficult subjects at the upcoming conference on the illegal wildlife trade in London in October is so important," he added.
He called on global leaders to put an end to wildlife crime in Africa, saying it is an "international problem" that needs decisive action.
He added that any solutions must be worked out in partnership with local communities who are working to combat the scourge of poaching which has decimated rare animals such as black rhinos on the continent.
The critically endangered species have been hunted by poachers who supply their horns to Asia where they are sometimes used for medicinal purposes.
"The latest figures show that a rhino is killed every seven hours. The Illegal wildlife trade is an international problem that requires determined political leadership," the Duke of Cambridge said.
"Whatever approach we take to end wildlife crime, it must be based on evidence of what works on the ground with local communities," he added.
Prince William was received by Vice President Nangolo Mbumba and beneficiaries of the Commonwealth government scholarship programs when he arrived in the country on Monday.
From Namibia, the prince who is on a private working tour as president of United for Wildlife and patron of Tusk, a conservation group with projects across Africa, will also visit Tanzania and Kenya.