President Barack Obama's nominee to lead the FBI forcefully argued to the Senate that the oversight mechanisms on the government's widespread surveillance of phone records and online habits sufficiently protect Americans' privacy.

James Comey, the former US deputy attorney general, said Tuesday that the secret surveillance court that approves wiretapping requests is "anything but a rubber stamp", even though the so-called Fisa court approves nearly every surveillance request by the government.

"I think folks don't understand that the FBI operates under a wide variety of constraints," Comey testified during his confirmation hearing to succeed Robert Mueller as the second director of the bureau since 9/11. The combination of the Fisa court, investigative guidelines from the US attorney general, congressional scrutiny and internal inspectors general are "very effective" at checking FBI abuse, Comey argued.

The Senate judiciary committee's consideration of Comey occurred amid the backdrop of revelations from the Guardian and the Washington Post that the National Security Agency, with the co-operation of the FBI, is collecting the phone records of millions of Americans who are not under investigation for any crime. At the Justice Department in 2004, Comey famously rebelled against a Bush administration warrantless surveillance effort, now revealed to involve the bulk collection of Americans' online habits.

But Comey declined to criticize the broad, ongoing collection of the phone records when senators asked if they should be scaled back.

Having been out of government since 2005, Comey said that he was "not familiar with the details of the current programs" and did not wish to opine on them. "I do know, as a general matter, the collection and analysis of metadata is a valuable tool in counter-terrorism."

A secret 2009 draft report by the NSA inspector general – one of the internal watchdogs Comey cited as "very effective" – found that the programs have not changed substantially since Comey left the Justice Department in August 2005. The major difference is that now the collection and analysis of phone and internet "metadata" receives the blessing of the Fisa court, albeit without a specific finding that the bulk collection targets people suspected of a crime.

"I can only say with confidence that it's very important for the next director to continue the transformation of the FBI into an intelligence agency," Comey told the Senate panel.

The former deputy attorney general and federal prosecutor hedged on describing the priorities for his prospective 10-year tenure at the helm of the US's top law enforcement and domestic intelligence arm, contending he wanted to review the bureau internally before committing himself publicly to an agenda.

But Comey said he would be a "voice for transparency", especially when it came to declassifying the secret opinions of the Fisa court, which senator Richard Blumenthal blasted for secretly making law by "fiat". Comey did not commit to advocating declassification, but said that if Americans understood more about the court's boundaries for surveillance "they would feel better about it".

Similarly, Comey pledged to protect whistleblowers within the bureau, but suggested that a so-called shield law protecting journalists from being compelled to reveal their sources contain an exception for national security cases. The majority of cases where journalists might face government compulsion to identify sources involve national security information. The Obama administration, after criticism for its aggressive prosecution of leakers and surveillance on journalists to catch them, is now pushing a shield law.

Comey also faced criticism for his role in signing off on a May 2005 Justice Department memo indicating that waterboarding, the act of pouring water over the nose and mouth of a restrained person to induce a sense of drowning, might be legal. Comey explained that "as a person, a father, a leader, I thought it was torture", but had difficulty refuting the specific legal points, and instead "I fought the policy battle" within the administration to stop the practice.

Several senators, particularly Democrats, found Comey's waterboarding answers curious: "That was in a memo you approved," noted Al Franken – but none expressed opposition to Comey's nomination.

Instead, Comey's hearing, nearly three hours long, occasionally seemed like a coronation. Blumenthal said Comey enjoyed "very solid support" on the committee. Comey made self-deprecating jokes and slipped into colloquialisms. Queried about the FBI's current practice of reading emails older than 180 days without a warrant, Comey said: "I don't think the fourth amendment has, like your yogurt, an expiration date."