"These reports are deeply concerning and raise questions about whether our constitutional rights are secure," Patriot Act co-author Rep. James Sensenbrenner wrote in a letter to Attorney General Eric Holder.
Sensenbrenner, a Wisconsin Republican, said he was "extremely disturbed by what appears to be an overbroad interpretation of the act."
A day after the initial Guardian report on the Verizon court order, the Guardian and the Washington Post published reports alleging the NSA is able to tap into data held by some of the world's biggest online services companies as it hunts for terrorists.
The program, which the newspapers said is called PRISM, reportedly allows NSA analysts access to computers at Microsoft, Google and other companies to extract details of customer activities, including "audio and video chats, photographs, e-mails, documents" and other materials, The Post reported.
The Post reported PRISM, founded in 2007, has become the leading source of raw material for the NSA.
Clapper did not directly confirm the program's existence but acknowledged that the Post and Guardian stories "refer to collection of communications pursuant to Section 702 of the Foreign Intelligence Surveillance Act."
That section of the law authorizes intelligence agencies to collect information on non-U.S. residents as part of efforts to gather foreign intelligence.
He said the program cannot be used to target anyone inside the United States or U.S. citizens anywhere in the world and includes "extensive procedures, specifically approved by the court, to ensure that only non-U.S. persons outside the U.S. are targeted, and that minimize the acquisition, retention and dissemination of incidentally acquired information about U.S. persons."
"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," Clapper said Thursday.
"The unauthorized disclosure of information about this important and entirely legal program is reprehensible and risks important protections for the security of Americans," he said.
While the Post initially reported that the companies "knowingly participate" in the program, it later updated the online version of its story to remove that contention.
In its stead, the newspaper described a classified report indicating that NSA analysts were allowed to send "content tasking instructions directly to equipment installed at company-controlled locations."
AT&T, Verizon and Comcast declined to comment on the report Friday. Time Warner said it was unfamiliar with PRISM.
Microsoft said Thursday that it doesn't participate in any national security data gathering program. Facebook and Google said they do not give government agencies direct access to their servers.
And Apple spokesman Steve Dowling said his company has never heard of the program.
While controversial to some, the programs also have plenty of backers. Obama noted that Congress has repeatedly endorsed the programs on a bipartisan basis.
Conservative Sen. Lindsey Graham, a Republican from South Carolina, and Sen. Dianne Feinstein, a California liberal, both believe the methods are necessary to prevent terrorism.
"Terrorists will come after us if they can," Feinstein said, "and the only thing that we have to deter this is good intelligence to understand that a plot has been hatched and to get there before they get to us."
Graham said that as a Verizon customer, "it doesn't bother me one bit for the National Security Agency to have my phone number."
Similar efforts have floated to the surface for years.
After the 2001 terrorist attacks, President George W. Bush's administration authorized the NSA to conduct wireless surveillance of international phone calls that included at least one person believed to be an al Qaeda-affiliated terrorist.
The program was later ruled unconstitutional.