Patients with pacemakers are generally discouraged from having MRI scans because the radio waves could interfere with the functioning of their device.
However, in documents posted online, the FDA complained that the company's study suffered from a small population size and missing data.
Minneapolis-based Medtronic enrolled more than 500 patients with pacemakers and randomly assigned half of them to receive an MRI scan. Those patients were free of MRI-related complications, achieving the study's goal.
But the FDA said the company did not provide detailed follow-up on many patients who enrolled in the study.
Medtronic said in a statement that some data were missing "due to that patient's condition," but that had no effect on the study results. The company also disputed the FDA's comments about the small size of the study.
"We worked closely with the FDA in the design of our clinical trial and exceeded the minimum number of required trial participants," said company spokesman Chris Garland.
The FDA will ask a panel of outside experts Friday whether Medtronic's study showed the Surescan pacemaker is safe and effective.
The agency is not required to follow the group's advice, though it often does.
Magnetic Resonance Imaging is one of the most widely used scanning technologies in medical practice. Physicians use the technique to diagnose problems in the brain, heart and other organs.
Pacemakers are implanted under the skin of the chest and use electric pulses to maintain a steady heart rhythm.