Sweeping up Americans' telephone records and monitoring Internet activity from overseas are "modest encroachments on privacy" that can help US intelligence analysts disrupt terror activity, he said during a four-day trip to the West Coast.
"Nobody is listening to your telephone calls," he reassured Americans worried about the prospect of government agents listening in on private conversations, CNN reported.
"That's not what this programme is about," he said in his first comments since the media revelations of programmes to collect information about phone calls and Internet traffic.
Obama said the programmes help prevent terrorist attacks and they are kept in check by rigorous judicial and Congressional oversight.
He acknowledged that the public may be uncomfortable with the broad reach of the formerly secret programmes, but he said he believed the government had struck the right balance between the need to fight terrorism and the need to protect privacy.
"You can't have 100 per cent security and then also have 100 per cent privacy and zero inconvenience," Obama was quoted as saying by the New York Times.
He repeatedly stressed that the lawmakers from both parties and federal judges were aware of the efforts. "You know, we're going to have to make some choices as a society."
"If the intelligence community actually wants to listen to a telephone call, they have to go back to a federal judge," Obama was quoted as saying.
The collection of information from Internet companies like Google and Apple does not apply to American citizens or people living in the United States, he said.
Obama also repeatedly stressed that the surveillance programmes were subject to Congressional oversight, according to the Times.