Potential side effects are too severe, and available vaccines have not been tested on children, who may be at higher risk for bad reactions, the academy said in a policy statement released Monday.
"We're talking about a disease that hasn't existed in the world since the 1970s and a vaccine that we know can cause death," said Dr. Julia McMillan, a Johns Hopkins School of Medicine pediatrics professor and co-author of the policy.
Based on studies from the 1960s, 15 out of every million people vaccinated will face life-threatening reactions, and one to two will die.
"Anybody who comes in contact with a person who's been vaccinated could be inadvertently infected with the vaccinea virus," Dr. Robert Baltimore, a member of the Academy's Committee on Infectious Diseases, told CBS Radio News. "If, say, you choose not to be immunized, but people around you are immunized, there is a concern that the virus could spread to you."
The academy's policy is considerably more conservative than one being finalized by the Bush administration, which plans to offer the vaccine to all 280 million Americans.
No final decisions have been made, with debate inside the administration centering on how quickly to make the vaccine available.
The academy says unless there's a high risk of a smallpox attack, it makes more sense to vaccinate only if someone becomes infected. It recommends first vaccinating people closest to the infected patient, then others with whom those people and the patient may have come in contact.
A similar strategy of "ring vaccination" in the 1960s and 1970s eradicated smallpox worldwide, the academy said, noting that the last known case occurred in 1977 in Somalia.
"That's the model for the successful eradication of smallpox throughout the world," said Baltimore. "Ring vaccination is how smallpox became a disease of the past."
The national Centers for Disease Control and Prevention supports ring vaccination to control any outbreak, though officials have asked communities to also prepare for mass vaccinations.
The United States discontinued routine childhood immunization against smallpox in 1972.
Potential vaccine side effects range from severe rashes to encephalitis and death.
If all Americans are vaccinated, the number of severe reactions likely would be higher than in the past because there may be more people with ailments such as HIV infections that make them more vulnerable, the policy says.
Federal officials note, however, that screening for such ailments may be better today than in the 1960s.