The director of national intelligence was responding to articles about an alleged secret programme, Prism.
The Washington Post said US agencies tapped directly into the servers of nine internet firms to track people.
But leading US internet giants denied giving government agents direct access to their central servers.
The reports about Prism will raise fresh questions about how far the US government should encroach on citizens' privacy in the interests of national security.
Earlier on Thursday, the National Security Agency (NSA) confirmed that it had been secretly collecting millions of phone records.
Prism was reportedly developed in 2007 out of a programme of domestic surveillance without warrants that was set up by President George W Bush after the 9/11 attacks.
Prism reportedly does not collect user data, but is able to pull out material that matches a set of search terms.
In a statement late on Thursday, Mr Clapper said reports by the Washington Post and by the Guardian about Prism contained "numerous inaccuracies," although he did not offer any details.
He said the communications-collection programme was "designed to facilitate the acquisition of foreign intelligence information concerning non-US persons located outside the United States".
"It cannot be used to intentionally target any US citizen, any other US person, or anyone located within the United States," he added.
Mr Clapper said the programme, under Section 702 of the Foreign Intelligence Surveillance Act, was recently reauthorised by Congress after hearings and debate.
"Information collected under this program is among the most important and valuable foreign intelligence information we collect, and is used to protect our nation from a wide variety of threats," he added.
But while US citizens were not intended to be the targets of surveillance, the Washington Post says large quantities of content from Americans are nevertheless screened in order to track or learn more about the target.
The data gathered through Prism has grown to become a major contributor to the president's daily briefing and accounts for almost one in seven intelligence reports, it adds.
The Washington Post named the nine companies participating in the programme as Microsoft, Yahoo, Google, Facebook, PalTalk, AOL, Skype, YouTube and Apple.
Microsoft said in a statement to the BBC that it only turned over customer data when given a legally binding order, and only complied with orders for specific accounts.
"If the government has a broader voluntary national security program to gather customer data we don't participate in it," Microsoft said.
Meanwhile, Yahoo, Apple and Facebook said they did not give the government direct access to their servers.
In a statement, Google said: "Google does not have a 'back door' for the government to access private user data."
On Wednesday, it emerged that the NSA was collecting the phone records of tens of millions of Americans, after the Guardian published a secret order for the Verizon phone company to hand over its records.
Mr Clapper said late on Thursday that the report about the court order "threatens potentially long-lasting and irreversible harm to our ability to identify and respond to the many threats facing our nation".
A senior congressman, House intelligence committee chairman Mike Rogers, told reporters that collecting Americans' phone records was legal, authorised by Congress and had not been abused by the Obama administration.
He also said it had prevented a "significant" attack on the US "within the past few years", but declined to offer more information.
The order requires Verizon - one of the largest phone companies in the US - to disclose to the NSA the metadata of all calls it processes, both domestic and international, in which at least one party is in the US.
Such metadata includes telephone numbers, calling card numbers, the serial numbers of phones used and the time and duration of calls. It does not include the content of a call or the callers' addresses or financial information.