The company later told CNBC that it is aware that the office is working with the Justice Department and the U.S. attorney for Massachusetts on a previously disclosed inquiry.
In that investigation, the federal prosecutor sought documents related to organizations that "provide financial assistance to Medicare patients taking drugs sold by Alexion" and the company's ties to these organizations. Alexion said it is cooperating with that investigation.
Alexion said it hasn't received a separate subpoena from the inspector general for any other matter.
The stock fell nearly 5 percent, before recovering some of those losses. Shares ended the day about 3 percent lower.
Don White, spokesman for the office of the inspector general, told CNBC: "As a matter of standard law enforcement procedure, OIG neither confirms nor denies investigations that may – or may not – be pending before the agency."
— CNBC's Meg Tirrell contributed to this report.