Attempting to persuade the Senate that he will reform the Department of Homeland Security, Barack Obama’s nominee to run the beleaguered agency warned that contemporary terror threats were growing harder to track.

Jeh Johnson, the former top Pentagon lawyer, said that the US was facing a “more diffuse” threat of terrorism, and feared that the US faced a “blind spot” in tracking the foreign travel of suspicious Americans – although he said that the Department of Homeland Security needed vigilance in protecting civil liberties.

“We have a problem with suspicious individuals laundering their travel,” Johnson said.

But Johnson focused most of his energy at his nomination hearing on pledging to better manage a sprawling bureaucracy with responsibilities ranging from counterterrorism to border security to immigration, and cited a need to improve departmental morale.

While committing himself to few substantive policy changes, Johnson told the Senate homeland security and government affairs panel that he at times was an outlier in administration debates, including on counterterrorism.

“It felt like it was eleven to one, and I was the one,” Johnson said.

Addressing the use of advanced surveillance technology for border security, including the department’s fleet of about a dozen unarmed drones, Johnson said DHS needed “to also be sensitive to privacy and civil liberties concerns that people who live along those borders have.”

Ahead of the hearing, a coalition of civil libertarians urged senators to “seek clarification of Mr Johnson’s views on the legal authority for and scope of the targeted killing program.”

While Johnson had a reputation as one of the most liberal members of Obama’s counterterrorism team, he argued in a 2011 speech that “belligerents who happen to be US citizens do not enjoy immunity” from what the administration calls a “targeted killing” program.

Yet drone strikes and many other counterterrorism issues – the sole rationale for the creation of DHS ten years ago – were barely mentioned at the hearing, which was dominated by discussions of the department’s myriad challenges with sensible spending, immigration enforcement and leadership vacancies.

Not until New Hampshire Republican Kelly Ayotte queried Johnson, some 90 minutes into the hearing, did Johnson present an assessment of domestic terror threats.

Johnson said the domestic terror threat was “moving into a third phase,” in which threats were “becoming more diffuse” and marked by self-radicalization, rather than actual affiliation with a terrorist group.

“Those threats in my view are even harder to detect, [and] we’re going to have to be vigilant,” Johnson said.

The former Air Force lawyer was faced with sharp questions on his views on privacy and due process from senator Rand Paul, the Kentucky Republican and civil libertarian. Johnson was noncommittal when asked about bulk surveillance and killing Americans abroad suspected of terrorism.

“In the executive branch and in the Fisa Court, we need to be skeptical, we need to have robust discussions. I’ve been a part of that,” Johnson said.

“Due process isn't good people in a room discussing whether to kill someone,” Paul replied.

Johnson also wrestled with what he called a “blind spot” in current domestic counterterrorism: tracking the foreign travel of suspicious individuals, an issue that caused an uproar in the spring when the administration confirmed that the Boston Marathon co-bomber, Tamerlan Tsarnaev, had traveled to Russia for six months in 2012.

“I’m not necessarily saying we need to track the travel of every person that leaves this country,” Johnson said, citing “real privacy issues” that would cause an “uproar.”

But Johnson did signal an openness to greater surveillance measures: “Getting to a better place obviously involves a balance, and I recognize that.”

Johnson committed more to studying DHS’ vexing challenges than shifting any specific policy. Senator Tom Coburn, the Oklahoma Republican on the panel who has emerged as a chief critic of DHS’ performance, extracted a rare promise from a nominee to helm a security department to bolster his agency’s efficiency at a core function – specifically on cybersecurity – before asking for new authorities.

Coburn also lambasted DHS for disbursing “less than 25%” of its grant money to state and local law enforcement that face minimal security threats. DHS announced in August that its current grant program amounted to $1.5bn annually, and it has given its various partners some $38bn since 2002.

Johnson faces little confirmation trouble. The three previous DHS secretaries – Republicans Tom Ridge and Michael Chertoff and Democrat Janet Napolitano – issued a letter to the committee this week endorsing Johnson.

Even John McCain, the Arizona Republican and 2008 GOP presidential nominee, hectored Johnson about border security but recognized “you will be taking on these new responsibilities.”