A troubled heart pump that has now been linked to 49 deaths and dozens of injuries worldwide will be allowed to remain in use, despite the Food and Drug Administration’s decision to issue an alert about the risk that it could puncture a wall of the heart.

The tiny Impella pumps, about the width of a candy cane, are threaded through blood vessels to take over the work of the heart in patients who are undergoing complex procedures or have life-threatening conditions.

The F.D.A. said the manufacturer of the device, Abiomed, should have notified the agency more than two years ago, when the company first posted an update on its website about the perforation risk. Such a notice, the F.D.A. added, would have led to a much broader official agency warning to hospitals and doctors.

The alert is the latest of concerns raised in recent years about the deadly side effects of cardiac devices, especially those that take over the heart’s role in circulating blood. It is the third major F.D.A. action for an Impella device in a year.

A series of studies suggested that the Impella heart devices heighten the risk of death in patients with unstable medical conditions. Meanwhile, the device maker has spent millions of dollars promoting the device and awarding consulting payments to cardiologists and grants to hospitals.

Since Abiomed’s first notice about the Impella’s complications in October 2021, the F.D.A. received 21 additional reports of heart-wall tears linked to patient deaths, according to Audra Harrison, a spokeswoman for the agency.