The FDA said it "has significant concerns of bacterial contamination" in the test kit solution in some Pilot COVID-19 At-Home Tests.
Using the contaminated solution "may pose safety concerns" as well as cause the test to give an inaccurate result.
BBC reports the agency warned tests should be thrown out immediately.
Over 500,000 tests were distributed to the CVS drugstore and around 16,000 were distributed to Amazon.
None were made available through one of the federal government's testing programmes.
Contaminated tests can be verified by the lot numbers on the FDA's website.
The liquid in the test kits was found to be contaminated "with organisms such as Enterococcus, Enterobacter, Klebsiella and Serratia species" that could cause illness for people with weakened immune systems, the FDA said.
It urged people to be vigilant "for signs of bacterial infection", which could include "fever, discharge, red eyes, or any other concerning symptoms".
Evie Baik, a spokesperson for SD Biosensor, told the BBC's US partner CBS News that raw materials from one of their suppliers is the likely source of the bacteria. They have cut ties with that supplier and are tightening quality control efforts.
The issue "was identified during routine quality assurance testing", Roche said in a statement, according to CBS News.
SD Biosensor and distributor, Roche, have said they are cooperating with the FDA and are working with distributors and retailers to hold back tests while the matter is investigated.