Hagel said he acted in response to a recommendation sent to him Tuesday by Army Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff, on behalf of the heads of each of the military services. They cited numerous factors, including concerns among military families and the communities from which troops are deploying for the Ebola response mission.
Just over 1,000 U.S. troops are in Liberia and Senegal supporting efforts to combat the virus.
Hagel also directed the Joint Chiefs to provide him within 15 days a detailed implementation plan for how the supervised isolation of troops will be applied.
He also ordered the chiefs to conduct with 45 days a review of this new regimen, which Hagel called "controlled monitoring."
"This review will offer a recommendation on whether or not such controlled monitoring should continue based on what we learn and observe from the initial waves of personnel returning from Operation United Assistance," Hagel's spokesman, Rear Adm. John Kirby, said in a written statement, using the official name of the military mission against Ebola in Africa.
"The secretary believes these initial steps are prudent given the large number of military personnel transiting from their home base and West Africa and the unique logistical demands and impact this deployment has on the force," Kirby added. "The secretary's highest priority is the safety and security of our men and women in uniform and their families."
The Army, acting on its own, put a small number of returning soldiers on a 21-day quarantine in Italy earlier this week.