"When it comes to telephone calls, nobody is listening to your telephone calls. That's not what this programme's about," Obama said in response to a question at a public meeting in California where he is travelling.
Defending his administration's decisions in this regard, including seeking information about internet and email usage of foreigners, Obama asserted that this has helped the US prevent terrorist attacks.
"What the intelligence community is doing is looking at phone numbers and durations of calls. They are not looking at people's names, and they're not looking at content," Obama said.
"But by sifting through this so-called metadata, they may identify potential leads with respect to folks who might engage in terrorism," he said.
"If the intelligence community then actually wants to listen to a phone call, they've got to go back to a federal judge, just like they would in a criminal investigation. So I want to be very clear. Some of the hype that we've been hearing over the last day or so -- nobody's listening to the content of people's phone calls," the US president clarified.
His assurances came amid reports appearing in several media outlets -- The Washington Post and Guardian -- that the US intelligence agencies have been secretly taking information on foreigners overseas for years from companies like Google, Facebook and Apple in search of security threats.
"We strongly object to using that power in this manner," The New York Times said in an editorial.
"The administration has now lost all credibility. Mr Obama is proving the truism that the executive will use any power it is given and very likely abuse it," the daily said.
In a report, The Washington Post said under the programme codenamed PRISM, the National Security Agency and the FBI are tapping directly into the central servers of nine leading US Internet companies -- Microsoft, Yahoo, Google, Facebook, PalTalk, AOL, Skype, YouTube, Apple - extracting audio and video chats, photographs, e-mails, documents, and connection logs that enable analysts to track foreign targets.
"The court-approved programme is focused on foreign communications traffic, which often flows through US servers even when sent from one overseas location to another," the report said.
The companies, however, denied such allegations, arguing that they are not providing any such assistance to the US government.
"We have never heard of PRISM. We do not provide any government agency with direct access to our servers, and any government agency requesting customer data must get a court order," Apple spokesman Steve Dowling said.
The secretive programme, now out in the media, Obama argued is fully overseen not just by Congress but by the FISA Court, a court specially put together to evaluate classified programmes to make sure that the executive branch, or government generally, is not abusing them and that it's being consistent with the Constitution and rule of law.
Obama said seeking information about use of internet and emails, does not apply to US citizens.
"With respect to the Internet and emails, this does not apply to US citizens, and it does not apply to people living in the US. And again, in this instance, not only is Congress fully apprised of it, but what is also true is that the FISA Court has to authorise it," he said.
Both the programmes, Obama said, have been authorised by the Congress.
"In summary, what you've got is two programmes that were originally authorised by Congress, have been repeatedly authorised by Congress, bipartisan majorities have approved on them, Congress is continually briefed on how these are conducted, there are a whole range of safeguards involved, and federal judges are overseeing the entire programme throughout," the US President said, adding that his administration has set up an audit process.
At the same time Obama said the two programmes have prevented terrorist attacks.
"My assessment and my team's assessment was that they help us prevent terrorist attacks and the modest encroachments on privacy that are involved in getting phone numbers or duration without a name attached and not looking at content that on, you know, net, it was worth us doing. Now, some other folks may have a different assessment of that," he said.
"I think it's important to recognise that you can't have 100 per cent security and also then have 100 per cent privacy and zero inconvenience. You know, we're going to have to make some choices as a society," he noted.
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