Mr Obama called the strikes a “targeted focused effort at people who are on a list of active terrorists”.
The US does not routinely speak publicly about drone operations.
Mr Obama made his comments during an hour-long video “hangout” on Google’s social network, Google+, which was also streamed live on YouTube.
Asked about the use of drone strikes, which have increased in intensity during his presidency, he said “a lot of these strikes have been in the Fata”, or Pakistan’s Federally Administered Tribal Areas.
The strikes target “al-Qaeda suspects who are up in very tough terrain along the border between Afghanistan and Pakistan,” Mr Obama added.
“For us to be able to get them in another way would involve probably a lot more intrusive military action than the ones we’re already engaging in.”
Few details are known about the covert US drone operation, which is run by the CIA and targets al-Qaeda and Taliban militants in the mountainous areas along the Afghan-Pakistan border.
According to the AFP news agency, 64 US missile strikes were reported in the area in 2011, down from 101 in 2010.