The White House announced on its Web site Tuesday that Malia, 11, and Sasha, 8, got the shots from a White House doctor last week.
The doctor, who was not identified, applied for and received the vaccine from the city's health department "using the same process as every other vaccination site in the District" of Columbia, said Katie McCormick Lelyveld, a spokeswoman for first lady Michelle Obama.
McCormick Lelyveld said the president and Mrs. Obama would wait to get their shots until after people in priority groups, such as children, young adults and pregnant women, have been vaccinated against the strain of flu known as H1N1.
News that the Obama sisters have received their swine flu shots was likely to raise questions about whether they had been given preferential treatment. It also could anger parents who are having difficulty getting shots for their own children because of shortages in the promised vaccine production and the way the vaccine that is available is being distributed.
At the same time, Obama has been urged to vaccinate the girls to encourage parents skeptical about the vaccine's safety to do the same.
Obama last week declared the swine flu outbreak a national emergency, and gave his health secretary power to let hospitals move emergency rooms offsite to speed treatment and protect patients not infected with the virus.
U.S. health officials said Tuesday that more than 22 million doses of swine flu vaccine are now available and that most people should soon begin to find it easier to get a shot.
Last week, just 14 million doses were on hand, despite initial government predictions that as many as 120 million would be ready by mid-October. The government later slashed that estimate to 45 million. The slow supply has frustrated members of the public, many of whom have stood in line for hours at vaccine clinics around the country.
Health authorities say the H1N1 virus has killed more than 1,000 people in the United States, and 46 states have widespread flu activity.
All four of the Obamas already have received their seasonal flu shots.