Counterinsurgency analyst Bill Roggio, who writes at the online Long War Journal, said the recently retired general was frustrated with work of the CIA and the Defense Intelligence Agency (DIA) before he took over as U.S. commander in Iraq.

“There were real tensions even when he was in Mosul,” said Mr. Roggio, referring to Mr. Petraeus‘ stint as commander of the 101st Airborne Division there during the first few years of the Iraq War.

After being confirmed as commander of all troops in Iraq in February 2007, the general “went on an end run around the CIA,” Mr. Roggio added, in an account whose broad outlines were privately confirmed by two former intelligence officials, including one who was working in Iraq at the time when Mr. Petraeus took command.

“He created his own intelligence shop. … My understanding is it was to get things done that CIA and DIA weren’t doing, not just analysis but to drive operations,” Mr. Roggio said.

“What he was doing in Iraq,” he added, referring to the surge of U.S. forces Mr. Petraeus led and the relationship he built with the Sunni tribal militias known as the Anbar awakening “ran counter to the analysis from both the CIA and the DIA” about the relationships within the insurgency and the role of al Qaeda in Iraq.

Current officials disputed that picture and played down any tensions in Baghdad, saying they were no more than workaday bureaucratic frictions.

“Analytical differences over complex issues and trends are part of everyday life in the intelligence business. Unfortunately, some people blow these natural and healthy differences into bureaucratic clashes that simply don’t exist,” said one official, adding that the idea that Mr. Petraeus created a military unit to end-run intelligence agencies is “ridiculous.”

Indeed, in recent public statements, Mr. Petraeus, while noting some disagreements with CIA assessments, praised the agency and its staff.

“I have the absolute highest regard for you and for this agency,” Mr. Petraeus told CIA employees all over the world by videoconference Tuesday. “I believe it’s one of the greatest concentrations of talent and capability that our country has,” he concluded.

At his June confirmation hearing to be CIA director, however, Mr. Petraeus noted several occasions when he differed with significant CIA assessments of the situation on the ground where he was commander. For instance, he said, some estimates were outdated in September 2007 on Iraq and in December 2010 on Afghanistan.

“In each case, my team and I felt that the situation had changed significantly following the intelligence community assessment cutoff date, typically some six to eight weeks prior to the date of the assessment being reviewed by the president,” he told the Senate Select Intelligence Committee. “In view of that, we sought to provide our assessment and more up-to-date analysis,” to policymakers, he said.

“However,” he stated, “if confirmed, when I am in the Situation Room with the president, I will strive to represent the agency position.”

“My goal has always been to speak truth to power,” he said, “and I will strive to do that as director of the CIA, if confirmed.”

Mr. Petraeus also sought to assuage concerns that he would bring his own “military brain trust,” or close advisers, with him to CIA.

“There is no shortage of impressive individuals at the agency, and I look forward to interacting with them and populating my office with them. If confirmed, I will, in short, get out of my vehicle alone on the day that I report to Langley,” he said.

As the tempo of the agency’s lethal operations against al Qaeda in Afghanistan, Pakistan and elsewhere continue at a high rate, Obama administration officials are keen to see a smooth transition.

“We’re doing this today in the Roosevelt Room because there’s literally no time to waste,” said Vice President Joseph R. Biden. “The president wants him on the job, and I think we’re going to be going from here to right down stairs” to brief the president right away, Mr. Biden added.

One official told The Times that CIA Deputy Director Michael J. Morrell was likely to stay on and take on much of the day-to-day management of the agency.

Nonetheless, Mr. Roggio said, the history of conflict with some agency officials raised a question: “What happens, historically to directors who mix it up with the agency establishment?”

CIA Director Porter J. Goss, during the George W. Bush administration, for example, was undermined by agency officials who disagreed with his management style and disliked his close advisers who were critical of many career agency officials.

• Eli Lake and Bill Gertz contributed to this report.