Low levels of magnesium could increase the risk of leg spasms, arrhythmias and seizures.
The FDA's notice includes prescription PPIs and over-the-counter formulations of Prilosec, Zegerid and Prevacid.
Physicians are encouraged to check the magnesium levels of patients on the medications.
This latest warning follows reports linking PPIs to increased risk of bone fracture.
Another study found the drugs may increase the risk of an infection that can cause severe diarrhea.