In a study published last year in the journal Environmental Health Perspectives, researchers put five San Francisco families on a three-day diet of food that hadn’t been in contact with plastic.

When they compared urine samples before and after the diet, the scientists were stunned to see what a difference a few days could make: The participants’ levels of bisphenol A, or BPA, which is used to harden polycarbonate plastic, plunged – by two-thirds, on average – while those of the phthalate DEHP, which imparts flexibility to plastics, dropped by more than half.

The findings seemed to confirm what many experts suspected: Plastic food packaging is a major source of these potentially harmful chemicals, which most Americans harbor in their bodies. Other studies have shown phthalates passing into food from processing equipment and food-prep gloves, gaskets and seals on non-plastic containers, inks used on labels – which can permeate packaging – and even the plastic film used in agriculture.

The government has long known that tiny amounts of chemicals used to make plastics can sometimes migrate into food. The Food and Drug Administration regulates these migrants as “indirect food additives” and has approved more than 3,000 such chemicals for use in food-contact applications since 1958. It judges safety based on models that estimate how much of a given substance might end up on someone’s dinner plate. If the concentration is low enough (and when these substances occur in food, it is almost always in trace amounts), further safety testing isn’t required.

Meanwhile, scientists are beginning to piece together data about the ubiquity of chemicals in the food supply and the cumulative impact of chemicals at minute doses. What they’re finding has some health advocates worried.

This is “a huge issue, and no (regulator) is paying attention,” said Janet Nudelman, program and policy director at the Breast Cancer Fund, a nonprofit that focuses on the environmental causes of the disease. “It doesn’t make sense to regulate the safety of food and then put the food in an unsafe package.”

How common are these chemicals? Researchers have found traces of styrene, a likely carcinogen, in instant noodles sold in polystyrene cups. They’ve detected nonylphenol – an estrogen-mimicking chemical produced by the breakdown of antioxidants used in plastics – in apple juice and baby formula. They’ve found traces of other hormone-disrupting chemicals in various foods: fire retardants in butter, Teflon components in microwave popcorn, and dibutyltin – a heat stabilizer for polyvinyl chloride – in beer, margarine, mayonnaise, processed cheese and wine. They’ve found unidentified estrogenic substances leaching from plastic water bottles.

Finding out which chemicals might have seeped into your groceries is nearly impossible, given the limited information collected and disclosed by regulators, the scientific challenges of this research and the secrecy of the food and packaging industries, which view their components as proprietary information. Although scientists are learning more about the pathways of these substances – and their potential effect on health – there is an enormous debate among scientists, policymakers and industry experts about what levels are safe.

The issue is complicated by questions about cumulative exposure, as Americans come into contact with multiple chemical-leaching products every day. Those questions are still unresolved, said Linda Birnbaum, director of the National Institute of Environmental Health Science, part of the National Institutes of Health. Still, she said, “we do know that if chemicals act by the same pathway that they will act in an additive manner” – meaning that a variety of chemicals ingested separately in very small doses may act on certain organ systems or tissues as if they were a single cumulative dose.

The American Chemistry Council said there is no cause for concern. “All materials intended for contact with food must meet stringent FDA safety requirements before they are allowed on the market,” said spokeswoman Kathryn Murray St. John. “Scientific experts review the full weight of all the evidence when making such safety determinations.”

When it comes to food packaging and processing, among the most frequently studied agents are phthalates, a family of chemicals used in lubricants and solvents and to make polyvinyl chloride pliable. (PVC is used throughout the food processing and packaging industries for such things as tubing, conveyor belts, food-prep gloves and packaging.)

Because they are not chemically bonded to the plastic, phthalates can escape fairly easily. Some appear to do little harm, but animal studies and human epidemiological studies suggest that one phthalate, called DEHP, can interfere with testosterone during development. Studies have associated low-dose exposure to the chemical with male reproductive disorders, thyroid dysfunction and subtle behavioral changes.

But measuring the amount of phthalates that end up in food is notoriously difficult. Because these chemicals are ubiquitous, they contaminate equipment in even purportedly sterile labs.

Perhaps the most controversial chemical in food packaging is BPA, which is chiefly found in the epoxy lining of food cans and which mimics natural estrogen in the body. Many researchers have correlated low-dose exposures to BPA with later problems such as breast cancer, heart disease and diabetes. But other studies have found no association. Canada declared BPA toxic in October 2010, but industry and regulators in the United States and other countries maintain that health concerns are overblown.

Last month, the FDA denied a petition to ban the chemical.

The fact that a plastic bottle or bag or tub can leach chemicals doesn’t necessarily make it a hazard to human health. Indeed, to the FDA, the key issue isn’t whether a chemical can migrate into food, but how much of that substance consumers might ingest.

If simulations and modeling studies predict that a serving contains less than 0.5 parts per billion of a suspect chemical – equivalent to half a grain of salt in an Olympic-size swimming pool – FDA’s guidance does not call for any further safety testing.

On the premise that the dose makes the poison, the agency has approved a number of potentially hazardous substances for food-contact uses, including phosphoric acid, vinyl chloride and formaldehyde.

But critics now question that logic. For one thing, it doesn’t take into account the emerging science on chemicals that interfere with natural hormones and might be harmful at much lower doses than has been thought to cause health problems.

According to Jane Muncke, a Swiss researcher who has reviewed decades’ worth of literature on chemicals used in packaging, at least 50 compounds with known or suspected endocrine-disrupting activity have been approved as food-contact materials.

“Some of those chemicals were approved back in the 1960s, and I think we’ve learned a few things about health since then,” said Thomas Neltner, director of a Pew Charitable Trusts project that examines how the FDA regulates food additives.

Another criticism is that the FDA doesn’t consider cumulative dietary exposure.

“The risk assessments have been done only one chemical at a time, and yet that’s not how we eat,” said Arnold Schecter, an environmental health specialist at the University of Texas Health Science Center.

Others are concerned that the FDA relies on manufacturers to provide migration data and preliminary safety information, and that the agency protects its findings as confidential.

So consumers have no way of knowing what chemicals, and in what amounts, they are putting on the table every day.