Announcing the move, assistant secretary of defence for health affairs William Winkenwerder also said the US was resuming mandatory anthrax vaccinations of military personnel in high-risk areas.
This marks a change of the previous policy of vaccinating all the members of the armed forces, which had been scaled back due to the shortage of supplies.
The vaccines will not be available for civilians to buy.
The deaths from anthrax of five Americans, including postal and hospital workers, and the infection of 13 others late last year have fuelled demand for an effective vaccine.
Investigators are yet to attribute responsibility for the anthrax attacks, in which letters laced with the bacteria were sent to dozens of American targets in the US and abroad.
Shift
Mr Winkenwerder said Washington believed that the threat of an anthrax attack against US personnel remained real, but not all US troops would be inoculated.
He said the shots would be given to US military personnel, essential civilian defence officials or civilian contractors deployed for more than 15 days in high-threat areas and whose performance was essential to the mission.
Previously, the vaccine had been reserved for troops on special missions and researchers alone.
"This is a shift from an earlier policy which was to vaccinate everyone - a total force vaccination policy," Mr Winkenwerder said.
"Anthrax is highly lethal and it's easily stored; we know that potential adversaries do possess it," Mr Winkenwerder said.
He added that there was a domestic need for the vaccine to be set aside for civilians. Health department spokesman William Raub said the doses reserved for civilians would only be used in the event of a domestic anthrax exposure, in combination with antibiotics.
Mr Winkenwerder did not reveal how many troops would receive the vaccine.
"We think it's best to leave others guessing as to who and how many," he said.
Some US troops have refused to take the vaccine complaining of side effects, but Mr Winkenwerder said the jab was reliable and no deaths had resulted from the inoculations.