Army Maj. James Crabtree, a spokesman for the U.S. jail facility in southeast Cuba, said the doses should start arriving this month, with guards and then inmates scheduled for inoculations.
He acknowledged there may be an "emotional response" from critics who argue that terror suspects should not be allocated swine-flu medications while members of the U.S. public are still waiting due to a vaccine shortage.
But he said U.S. military officials are "responsible for the health and care of the detainee population."
Medical personnel at Guantanamo requested the doses, but Crabtree said he did not know how many.
CBSNews.com Special Report: H1N1
Detainees will be vaccinated "entirely on a voluntary basis," he said. "There is always going to be a segment of the population that is going to refuse," either due to anxiety about a shot or to "distrust of our motivations."
The top House Republican, Rep. John Boehner of Ohio, told CNN's "State of the Union" show on Sunday that he does not agree with the H1N1 vaccination plans for detainees at Guantanamo.
"I don't think it's a good idea. The administration probably didn't think it would be very popular either; that's why they announced it on Friday night," Boehner said.
The Miami Herald first reported about the vaccination plans on Wednesday.
Health officials have recommended that people in high-risk groups receive the swine flu vaccination first. There has been heated debate in several U.S. states about where prisoners should fall in the pecking order of vaccine recipients.
A spokesman for Physicians For Human Rights, an international medical group, said there are "certain basic obligations the U.S. has to its prisoners," and that vaccinations for influenza fall into that category.
"The fact that many prisoners within the U.S. don't get timely access to basic health care doesn't change the obligation of the U.S. to prisoners at Guantanamo," Dr. Scott A. Allen of the rights group said in an e-mail from Rhode Island. "We should work towards securing H1N1 vaccine for all at-risk populations, and not towards lowering a public health standard for certain unpopular groups."
Following Saturday's transfer of six Chinese Muslims from Guantanamo to the tiny Pacific nation of Palau, roughly 215 detainees remain at the detention center. The Obama administration plans to prosecute some in U.S. courts and turn over others to nations willing to rehabilitate or free them.
The administration also is grappling with how to keep in prison a handful of remaining detainees who are considered too dangerous to release or put on trial.