President Bush received a recommendation yesterday from Defense Secretary Donald H. Rumsfeld to inoculate U.S. troops against smallpox but did not immediately accept it. One White House official said the Pentagon had not answered many of the president's questions.

"There's a lot of issues on both sides," the official said. "He's concerned not just about whether to do it, but how you do it. You don't want to do it if you can't do it right."

Another official compared Bush's contemplation about the issue to last year's agonizing over whether to allow federal funds to be used for research on stem cells from human embryos, since the issues involved are so grave and Bush is considering them so carefully.

The question of whether to immunize U.S. forces is part of a larger dilemma that includes whether to vaccinate civilian health care workers and, eventually, the general public. Although routine smallpox vaccinations stopped in the United States in 1972, the matter has gained new urgency amid heightened concerns about biological warfare and intelligence reports citing four nations, including Iraq and North Korea, as having covert stocks of the smallpox pathogen. But the vaccine itself has caused serious, sometimes fatal, complications in a very small percentage of recipients.

Pentagon officials have developed a plan for inoculating as many as 500,000 troops, with the first shots earmarked for emergency support troops such as medical specialists. Next in line would be troops designated for deployment in the Middle East and other areas in which the risk of combat is considered high, officials said.

Rumsfeld was described by an aide yesterday as strongly favoring the inoculation program, considering it critical to ensuring the protection of U.S. forces. But moving ahead with it has proved more problematic than a separate Pentagon effort that resumed last month to inoculate troops against anthrax.

The Department of Health and Human Services has set aside for the military about 1 million of the fewer than 2 million doses that have been licensed for use by the Food and Drug Administration. Senior federal health officials have recommended making the vaccine available in stages to the civilian population, beginning with people who work in hospital emergency rooms, followed by other health care workers and emergency responders and, ultimately, the public.