“This is a very unfortunate incident and highly regrettable,” the statement said. “We wish to express our sincere condolences to the bereaved family and friends of the deceased.”
No further details were provided about how the man died.
The ministry and police were investigating and hoped to establish whether the tour group had a guide, the statement said.
CNN has reached out to the Australian Department of Foreign Affairs and Trade for comment but is yet to receive a response.
Elephants in the Kunene region are known as desert elephants because they have adapted to its arid environment.
The ministry warned visitors to the country to “be cautious and adhere to the rules and regulations put in place for their safety.”