Bitter apricot kernels have become popular throughout the EU as a snack.
Regulators have been concerned about the way companies have been promoting the kernels as a health food.
Several websites have claimed that amygdalin fights cancer cells.
According to the BfR report, these health claims are unsubstantiated, and could "irresponsibly" encourage ill people to buy them.
Bitter apricot kernels have a high level of amygdalin.
Hydrocyanic acid, which is toxic, is released from the glycoside amygdalin during digestion.
This acid can lead to symptoms of poisoning like cramp, vomiting and respiratory distress, and may even provoke fatal respiratory paralysis at high doses.
The BfR scientific report said that eating more than only a few kernels per day can lead to the onset of these acute poisoning symptoms.
"Consumers should not, therefore, eat more than one or two bitter apricot kernels a day, or even none at all for precautionary reasons," the BfR advises.
It recommends that at the very least all customers should be made aware of the possible side-effects when they buy the product.
"At all events, consumers should be informed about the dangers of poisoning through warnings on the packaging", said Andreas Hensel, BfR's president.
The BfR is particularly concerned about the irregularity in the way the product is being packaged and sold over the internet.
It is difficult for official food control authorities to control this distribution channel.
The packs on sale differ in size and only some carry information about health risks, the report states.
Apricot kernels have caused concern for food agencies in the past, and several US food control authorities have banned the sale of inadequately labelled products.
In the UK, the Food Standard Agency expressed concern in April 2006 that when ingested, bitter apricot kernels can produce cyanide , and measures to regulate the direct consumption of bitter apricot kernels are currently being discussed on the European level.