Any adult or child who had blood drawn for a lead test since 2014 may have to be re-tested, the FDA said.
The agency also urged women who are now pregnant or nursing and were tested in this manner, to get retested.
"The FDA is deeply concerned by this situation and is warning laboratories and health care professionals that they should not use any Magellan Diagnostics' lead tests with blood drawn from a vein", Jeffrey Shuren, the director of the FDA Center for Devices and Radiological Health, said in the statement.
"While most children likely received an accurate test result, it is important to identify those whose exposure was missed, or underestimated, so that they can receive proper care", Patrick Breysse, director of the CDC's National Center for Environmental Health, said in a statement.
MDHHS said in a news release Wednesday that less than 2 percent of lead tests performed in MI since 2014 - including 128 in Flint - were done using Magellan equipment that processed blood drawn from veins.
The tests, manufactured by Magellan Diagnostics, are commonly used in doctors' offices and clinics, and on its website the company calls itself "the most trusted name in lead testing".More news: Purported Chibok girl 'escapes' Boko Haram
More news: Chelsea Manning to participate in documentary about her story
More news: Rory allays injury fears
The letter went on to urge that the tests "should not be submitted to the CT DPH for disease reporting purposes".
The agency "did not feel that the data was either adequate regarding what they thought may have been the cause of the problem, the extent of the problem or the effectiveness of the mitigation they put in place", the FDA's Shuren said.
Over 400,000 to 600,000 venous blood tests are conducted every year using Magellan technology, compared to more than 4 million finger or heel stick tests, said John Kraeutler, chief executive officer of Meridian Bioscience, Inc., the company that owns Magellan.
"There may be differences in how the blood is collected, the tubes that may be used for it, or some of the other processing, and that may account for why there are differences", he said. "Talk to your physician to determine if retesting is needed for your child".
Lead testing in children is typically done by a finger or heel stick known as capillary test. Candidates include anyone whose blood was drawn for the test and who had a blood lead level of 10 micrograms or less per deciliter. The FDA noted that it hadn't found any evidence of problems with the capillary blood samples.
Despite decades of USA progress in curbing lead poisoning, millions of children remain at risk.
The CDC website states that 4 million USA households have children that are exposed to high levels of lead and approximately a half-million children under the age of five have lead levels above 5 micrograms per deciliter (µg/dL), a level at which the agency recommends public health actions be taken. Lead can impair cognitive abilities and cause other damage in children.