Dr. Janet Woodcock, head of the FDA's Center for Drug Evaluation and Research, said the contaminant is oversulfated condroitin sulfate, a chemical that does not occur naturally.
Condroitin sulfate is a natural compound that occurs widely and is used as a dietary supplement but the oversulfated version has not been widely studied.
"We cannot rule in or out whether this was accidentally or deliberately introduced into the product," Woodcock said, "We are investigating how it got in."
The FDA has also initiated testing of imported heparin entering this country and Woodcock said the agency feels "doctors and patients now can be confident that the product on the market has been tested and is safe."
Condroitin sulfate is a compound in the same family as heparin, so preliminary testing did not identify it, Woodcock said. She said more exacting tests by the government and university researchers uncovered the contaminant.
Oversulfated condroitin sulfate would be less expensive to make than heparin, but FDA officials said they could not estimate the cost difference.
The lots of heparin linked to hundreds of allergic reactions were marketed by Baxter International and produced in China.
FDA said Chinese officials have been highly cooperative in the investigation.
The investigation comes just a year after melamine was identified as a contaminate in pet food from China. Officials said an agreement signed at that time with China helped smooth the way for this investigation.
FDA officials said they could not yet directly associate the oversulfated condroitin sulfate to the deaths and side effects, but it is the lone contaminant they have found in the product.
A different brand of heparin has also been recalled in Germany after 80 patients there became sick, and the German manufacturer said it was narrowing down the source of contamination to another Chinese supplier
On Wednesday, German regulators did not say if the contaminant they are investigating is oversulfated condroitin sulfate.
Heparin is derived from pig intestines, and China is the world's leading supplier. Tiny family-run workshops near slaughterhouses send batches of raw ingredients to larger middlemen before they reach factories.
Associated Press business writers Matthew Perrone in Washington and Matt Moore in Germany contributed to this report.