Days after the attack on Pearl Harbor, Scheele was dispatched to the Medical Division of the Federal Office of Civilian Defense, under New York City Mayor Fiorello H. LaGuardia.

Scheele closed out the war as director of the Health, Welfare, Education and Religion Division of the Allied Control Council in Berlin and received the U.S. Typhus Medal for his work in Germany.

Scheele's skilled diplomacy before the United States Congress in the spring of 1947 netted the National Institute of Health (NIH) a fourteenfold increase in budget appropriation.

Scheele also inherited projects begun before 1941, whose formal implementation had been delayed by the war, including the transfer of the Interior Department's health bureau for American Indians (1954), the transfer of the Department of Defense's Armed Forces Medical Library (1956, renamed the National Library of Medicine), and new programs to control water pollution (1948), ionizing radiation (1948), and air pollution (1955).

On the other hand, controversy surrounding failed batches of polio vaccine threatened to destroy public faith in the Federal health establishment.

Scheele and Department of Health, Education, and Welfare (DHEW) Secretary Oveta Culp Hobby released this long-awaited news at a press conference on April 12, 1955, the tenth anniversary of President Franklin Delano Roosevelt's death from complications of polio.

On April 27 he requested that one of the manufacturers, Cutter Laboratories, recall its vaccine and he created a new Poliomyelitis Surveillance Unit at the Communicable Disease Center (CDC) and a national infrastructure for case reporting from the states.

The following August (1956) Scheele resigned from his post as Surgeon General, to become President of Warner-Chilcott Laboratories, then part of the Warner-Lambert Company of Summit, New Jersey.

As a private sector executive, he continued to serve his country, for example, travelling to Cuba on behalf of the John F. Kennedy Administration, to arrange for the transfer of millions of dollars of medicines, public health and food supplies in exchange for the release of hostages taken during the failed Bay of Pigs Invasion.