PETA alleged Ramaphosa had a 50% stake in Tsala Hunting Safaris which organised elephant hunts through Wayne Wagner Safaris.
It was claimed Ramaphosa was "quietly developing and expanding a trophy hunting property called Diepdrift - stocking it with animals from his own wildlife breeding operation, Phala Phala - and he owned a 50% stake in Tsala Hunting Safaris".
"In other words, far from 'conserving' wildlife, wild animals are bred specifically to be killed for trophies. PETA recorded conversations in which Ramaphosa's managers admitted that he shares equally in the profits from all hunts conducted through Tsala and spoke of the importance of concealing his involvement," it claimed.
"President Ramaphosa's Tsala Hunting Safaris routinely organises elephant hunts through Wayne Wagner Safaris on properties of the Greater Kruger Conservancy."
A Presidency statement said: "The allegations are patently false and are refuted in full."
Comment was not immediately available from Tsala Hunting Safaris, and Wayne Wagner declined an opportunity to comment on PETA linking the company to Tsala Hunting Safaris.
In the video PETA posted, an elephant is seen buckling to its knees after a shot rings out in the bush. The claim is the elephant may have wandered away from the Kruger National Park.
The hunting guides instruct the shooter to adjust the level of the rifle and more shots are fired after the elephant sinks to its knees.
A claim by an anonymous source was made that Ramaphosa keeps his stake in the company secret to avoid bad publicity.
The Presidency said Ramaphosa did own Phala Phala Wildlife, which specialises in breeding rare game, but neither Ramaphosa nor Phala Phala has a stake in the industry or Tsala Hunting Safaris.
It added Phala Phala undertook annual culls of game such as impala, buffalo, kudu and wildebeest to avoid carrying excess numbers - part of an established wildlife management tool.
Phala Phala had entered into an agreement with Tsala Hunting Safaris to hunt the game "that would in any event have been culled".
However, in light of the allegations that Tsala hunts threatened or protected species on other properties, Phala Phala has given notice to Tsala Safaris to terminate the hunting arrangement with it.
"This decision is in line with Phala Phala's commitment to sound conservation principles, and its demonstrable compliance with ethical and lawful wildlife management standards."
The Presidency said PETA had previously made false allegations regarding Ramaphosa's interest in pigeon racing since the age of 16.
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