Researchers found toxic chemicals from recycled newspapers had contaminated food sold in many cardboard cartons.
The chemicals, known as mineral oils, come from printing inks.
Cereal firm Jordans has stopped using recycled cardboard and other firms are to ensure their recycled packaging does not contain any toxic oils.
Kellogg's and Weetabix said they were taking steps to reduce the amount of mineral oil in their packaging.
Exposure to mineral oils has been linked to inflammation of internal organs and cancer.
Government scientists in Switzerland found quantities of mineral oils between 10 and 100 times above the agreed limit in foods like pasta, rice and cereals sold in cartons made from recycled cardboard.
paper packaging , corrugated boxes , injection molded packaging , clamshells , clamshell packaging
Terry DonohoeFood Standards AgencyIn one scientific paper they describe the potential for mineral oils to migrate into foodstuffs as "frightening".
However, the Swiss food safety authorities have concluded that consumers who eat a balanced and varied diet have no need to worry.
In a statement Jordans said that, as an environmentally responsible company which had previously used largely recycled packaging, it had taken the decision to abandon it reluctantly, but felt it was sensible.
The BBC investigation found other food companies were aware of the issue - but none had so far followed Jordans' lead.
More than half the cardboard used in Europe is made from recycled materials.
So-called "virgin board" from newly harvested trees is more expensive and there is not enough of it to replace recycled card completely.
The research has been led by Dr Koni Grob at the government-run food safety laboratory of the Canton of Zurich.
In one study for the German food ministry last year he and his colleagues tested a sample of 119 products bought from German supermarkets.
They found mineral oils passed easily through many of the inner bags used to keep food dry and fresh.


