The Impella left sided pumps are used to temporarily support a patient's heart during high-risk procedures or after a severe heart attack.
But the regulator warned it could puncture a wall in the heart's left ventricle if used incorrectly.
The device's manufacturer, Abiomed, has issued new instructions for the pump.
A summary posted on the FDA's website on 21 March classified the move as "most serious type of recall" because of the risk of serious injuries or death if the device is used incorrectly.
The agency warned that the use of affected pumps may also cause serious adverse health consequences, including "hypertension, lack of blood flow, and death".
But it added that the recall was a correction, not a product removal, and the device will remain on the market.

US regulator issues highest alert for heart pump linked to 49 deaths (bbc.com)