Following a 2004 discussion paper on botanicals and botanical preparations, EFSA asked its scientific committee to prepare two compendia.
Comments will be accepted on both until February 15 2008.
In addition to guides on how this safety assessment can be done, EFSA has released two lists of plants.
The first contains more than 800 plants that are considered for food or food supplement use and that have been reported to contain toxic or addictive or psychotropic substances.
EFSA has not passed any opinion on whether these are suitable or not suitable for food in Europe.
Methods for how these can be substantiated have been put out for consultation.
The second list contains plants for supplements that have been reported to have a medicinal use.
The document is another step in the harmonisation of food laws across Europe.
EFSA said the guide is not to produce a list of safe botanicals and botanical preparations, but only to provide guidance on how to develop such a list.
The two lists are aimed at facilitating this.
For botanicals and botanical preparations with uses both as food supplements and medicinal products, a "case-by-case approach is needed for the safety assessment of their use as food supplements ", EFSA said.
This should include checking scientific evidence and evidence of traditional medicinal use, dose-response data, and anticipated intake.
The draft guidance also lays out how safety testing can be carried out, including methods for genotoxicity testing.
Brussels-based European Botanical Forum (EBF) said the move would remove existing grey areas, which gives the potential for some botanicals considered dangerous in one member state to be used in another.
In an interview with NutraIngredients.com earlier this month, EBF forum chairman Manfred Ruthsatz said: "You have some prohibited plants in some markets but the same plant can appear on a list in other countries."
Ruthsatz said there are some clear examples of botanicals never to appear in food supplements, such as foxglove.
He added: "This will establish clearly what can and can't be used, but also to create transparency in the process."