Rangers from Bwabwata National Park say more than 100 have died since last Sunday, many pictured with legs in the air as they lay bloated in the water.
Namibia's environment minister Pohamba Shifeta told news agency AFP that the country's veterinary services were working on establishing the exact cause.
"Our veterinary services are now working at the area to determine the cause of death".
"It happened in Zambia before and it mainly occurs when the level of the river is so low", said Colgar Sikopo, director of parks and wildlife management at Namibia's Ministry for the Environment and Tourism.
Anthrax is a deadly bacterial disease which is known to kill game, cattle, and sometimes humans.
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"We even saw the one in Tanzania, so as much as the numbers seem to be high, the hippo population usually recovers", he said.
It largely survives as spores that hide away in soil for years before entering an animal through a cut or wound. 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 hipposin Uganda in 2004.
Kannyinga said the first 10 deaths were reported on October 1 but had risen by the end of the week.
"I knew hippos were nasty, but I didn't know they went around eating each other", said anthrax expert Martin Hugh-Jones, a professor emeritus at Louisiana State University. Human deaths from anthrax in the US are extremely rare.
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.