"I think there is going to be lots of questions about, you know, leaks and detention and all the other things, as I talk to my friends in the Senate. It seems to be something that they're concerned about," Rogers said.
"I think at the end of the day, he gets confirmed for the position," the Michigan Democrat added.
But opposition to the Brennan pick has mounted in recent days, fueled by the unofficial release of a previously confidential Department of Justice (DOJ) white paper on Monday, justifying the use of armed drones against suspected terrorists who also may be U.S. citizens.
The paper, quietly distributed to Rogers and other select lawmakers last June, broadly outlined the criteria by which U.S. military or intelligence officials could launch drone strikes against terror suspects overseas, regardless of nationality.
During his time at the White House and CIA, Brennan played a key policy role in ushering in the aggressive use of targeted killings of suspected terrorists via armed aerial drone strikes.
Drone strikes have surged dramatically under President Obama, who has argued the tactic has been vital in U.S. efforts to dismantle the senior leadership of groups like al Qaeda in Afghanistan, Pakistan, Yemen and elsewhere.
Civil liberties groups argue the drone strikes sidestep or blatantly ignore constitutionally-guaranteed rights to due process in the name of national security.
The growing furor on Capitol Hill over the counterterrorism tactic prompted to Brennan to turn down the CIA nomination in 2008, paving the way for then Gen. David Petraeus to assume the post. Petraeus stepped down from CIA last year after admitting to an extramarital affair.
But Monday's leak of the DOJ white paper, first reported by NBC News, has reignited the drone debate and raised questions over Brennan's nomination.
While Rogers was fairly confident Brennan would secure the top spot at CIA, a number of senior lawmakers are indicating Brennan's confirmation is far from a done deal.
Sen. John Cornyn (R-Texas) has already threatened to hold up Brennan's confirmation, which is scheduled for Thursday, over concerns about unauthorized leaks of classified information on U.S. intelligence operations.
His request request for information from the DOJ on drone operations could provide more fodder for the Texas Republican's opposition.
Sen. Ron Wyden (D-Oregon), an outspoken critic of the U.S. drone program, has also hinted publicly that he would consider a filibuster over Brennan's nomination over the possible targeting of American citizens during U.S. counter-terror operations.
However, Rogers reiterated the ensuring controversy over the DOJ justification -- particularly the possible targeting of Americans -- would likely have little effect on Brennan's confirmation chances.
"What they were saying is, once you've made that choice, you no longer get the protections that you would," Rogers said regarding the DOJ arguments in the white paper.
"I mean, if you join the enemy overseas, you join the enemy overseas. And we're going to fight the enemy overseas," he said. "That's their choice, not ours."
His comments echoed those of White House press secretary Jay Carney, who said Tuesday all U.S. drone operations are "fully consistent" with U.S. law.
That said, Rogers noted that he, along with the House intelligence panel's ranking member Rep. Dutch Ruppersberger (R-Md.), as well as his counterparts on the Senate intelligence committee, are all briefed on U.S. armed drone operations worldwide.
"I knew about those operations, the targeting sets, all of that ... and I review all of the air strikes that we use under this title of the law," he said.