One of the activities in the game allows players to hunt and harpoon whales while sailing in their pirate ship, which PETA takes issue with.
"Whaling - that is, shooting whales with harpoons and leaving them to struggle for an hour or more before they die or are hacked apart while they are still alive - may seem like something out of the history books, but this bloody industry still goes on today in the face of international condemnation, and it's disgraceful for any game to glorify it," PETA said in a statement.
"PETA encourages video game companies to create games that celebrate animals - not games that promote hurting and killing them."
Ubisoft has responded to PETA with a statement of its own, telling GamesBeat: "History is our playground in Assassin's Creed.
"Assassin's Creed 4: Black Flag is a work of fiction that depicts the real events during the Golden Era of Pirates.
"We do not condone illegal whaling, just as we don't condone a pirate lifestyle of poor hygiene, plundering, hijacking ships, and over-the-legal-limit drunken debauchery."
Gallery: First images for Assassin's Creed 4 released:
Copyright: UbisoftConfirmed last week, Assassin's Creed 4 will be set in the Caribbean in 1715, with players taking control of Edward Kenway, the grandfather of Assassin's Creed 3 protagonist Connor Kenway.
Said to be the biggest Assassin's Creed game yet, it will feature 50 unique locations including the cities of Havana, Kingston and Nassau, as well as fishing villages, smugglers coves, plantations and jungles.
In a first for the series, players are able to explore underwater to search shipwrecks.
With Desmond's story concluded, the player themselves will assume the hero in the present day setting, working for Abstergo and researching Kenway's backstory.
Ubisoft recently revealed that the multiplayer modes will not offer naval battles, but that combat will also be more challenging than past games in the series.
Assassin's Creed 4: Black Flag will release November 1 in Europe and October 29 in North America on Xbox 360, PC, Wii U, the PS3 and PS4.
Both PlayStation platforms will also contain 60 minutes of exclusive content.
> Our extensive first-look preview of Assassin's Creed 4: Black Flag
Watch the first trailers for Assassin's Creed 4 below: