Namibia's environment minister Pohamba Shifeta told news agency AFP that the country's veterinary services were working on establishing the exact cause.
Anthrax is a bacteria disease caused by Bacillus anthracis, transmitted through spores which can lie in the soil for years.
"This is a situation that we have seen before", Colgar Sikopo, director of parks and wildlife management, says in a New Era article.
"The other mortalities are dispersed over the river, and the crocodiles and vultures are feeding on them", he said, adding that this is a natural phenomenon caused by the low waters in the Kavango River.
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According to the estimation from Government officials, before the mass death hippo population of Namibia was around 1,300. It can often be found in stagnant water, which would pose an obvious threat to semi-aquatic hippos during the dry season. There is also worry that humans will ingest the tainted flesh.
Anthrax outbreaks are fairly common among animals, even large mammals. More than 2,300 reindeer and a 12-year-old child were killed by anthrax during a heatwave in Siberia in August 2016, while anthrax claimed an estimated 300 hippos in Uganda in 2004.
Currently Namibian officials are focusing on preventing human exposure to the virus, by restricting contact with the dead hippos and suggesting locals not to eat them. Infected anthrax spores have also been used by bioterrorists in the recent past.
The most famous incident in the U.S. would be the 2001 attacks in which anthrax spores were mailed to multiple American newspapers, televised news outlets and Democratic senators.
The FBI accused United States government biodefense researcher Bruce Ivins of the crime shortly after his suicide.