The Scottish Code for Conservation Translocations is believed to be the first of its kind in the world and covers any plant, animal or fungus being moved from one area to another and released.
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The practice can reverse the extinction of a species, for example with red kites, or help individual animals and plants and make up for a decline in numbers caused by habitat loss or climate change.
But NFU Scotland's deputy director of policy Andrew Bauer said it did "not have the confidence that the current code will result in a balanced and rigorous assessment of potential reintroductions".
Launching the Code at the Scottish Game Fair in Scone, Minister for Environment and Climate Change Paul Wheelhouse said: "The guidelines are a world first- setting out the types of situation in which translocations may benefit wildlife, people and the environment, enabling thorough and transparent evaluation on a case by case basis."