WASHINGTON — With the appointment of a prosecutor to investigate detainee abuses, long-simmering conflicts between the Central Intelligence Agency and the Justice Department burst into plain view this week, threatening relations between two critical players on President Obama’s national security team.
The tension between the agencies complicates how the administration handles delicate national security issues, particularly the tracking and capturing of suspected terrorists overseas. It also may distract Mr. Obama, who is trying to move beyond the battles of the Bush years to focus on an ambitious domestic agenda, most notably health care legislation.
The strains became evident inside the administration in the past several weeks. In July, Leon E. Panetta, the C.I.A. director, tried to head off the investigation, administration officials said. He sent the C.I.A.’s top lawyer, Stephen W. Preston, to Justice to persuade aides to Attorney General Eric H. Holder Jr. to abandon any plans for an inquiry.
Mr. Preston presented what was, in effect, a closing argument in defense of the C.I.A., contending that many potential cases against intelligence operatives were legally flawed and noting that they had already been investigated, some more than once. In none, he said, had prosecutors found grounds for charges.
But the Justice Department was unmoved, officials said. Despite the C.I.A. pressure and the stated desire of the White House not to dwell on the past, Mr. Holder went ahead with an investigation that will determine whether agents broke the law in their brutal interrogations.
The officials interviewed for this article spoke anonymously so that they could discuss debates over classified matters.
On the day the decision was announced, Mr. Panetta phoned Mr. Holder, according to people familiar with the call. In the conversation, which lasted less than a minute, the C.I.A. director told the attorney general that the agency would cooperate but expressed his displeasure and swore mildly, if only once.
Mr. Holder and Mr. Panetta are each confronting difficult balancing acts. Mr. Holder inherited a dispirited department accused of carrying out the political wishes of the Bush White House, and he now must show independence while continuing to work with the rest of the administration.
For his part, Mr. Panetta, who is also new to his job and lacks a background in intelligence, must carry out White House orders to make a clean break with some of the Bush administration’s intelligence policies, including ending the C.I.A.’s harsh interrogations. At the same time he must soothe frayed nerves at the C.I.A.
Rahm Emanuel, the White House chief of staff, said that reports of shouting matches were overblown and that the protagonists were simply advocating for their agencies’ viewpoints in robust discussions, as they should. “Leon’s representing his institutional building,” Mr. Emanuel said. “Eric’s representing his institutional responsibilities.”
While top C.I.A. officials are angry at the Justice Department, Mr. Panetta has also quarreled over turf with Dennis C. Blair, the director of national intelligence, to whom he reports. The White House has occasionally been frustrated with both Mr. Panetta and Mr. Holder. And some in the administration have taken aim at Gregory B. Craig, the White House counsel, blaming him for some of the troubles in handling the detainee issue.
The behind-the-scenes fighting began in April when, in response to an A.C.L.U. lawsuit, the Justice Department prepared to release legal opinions written by its lawyers during the Bush administration authorizing the C.I.A. to use brutal interrogation techniques.
Mr. Obama disavowed the harsh methods, like waterboarding and wall-slamming, but the legal opinions were filled with embarrassing details about the C.I.A.’s aggressive approach. Mr. Panetta sought to heavily edit the memos before releasing them but was overruled when Mr. Obama sided with Mr. Holder, who wanted more detailed disclosures, the officials said.
Though he lost on the memos, Mr. Panetta’s camp came away thinking that at least they had won a tacit understanding, said some administration officials; the embarrassing details would be aired, but Justice would back off from any new investigation.
In April, C.I.A. officers felt reassured by Mr. Emanuel’s comments on ABC News, in which he said that Mr. Obama “believes that people in good faith were operating with the guidance they were provided; they shouldn’t be prosecuted.” But White House and Justice officials said that there was no such bargain and that all Mr. Emanuel meant was that C.I.A. officers who followed interrogation guidelines were safe from prosecution.
For his part, Mr. Holder had arrived in office in January thinking he might open an inquiry, and his resolve hardened after reading graphic classified reports of detainee abuse, including several deaths of prisoners in C.I.A. custody in Iraq and Afghanistan.Still, it came as a shock to the C.I.A. when Newsweek reported in July that Mr. Holder was leaning toward an investigation. Given that the information was contained in an exclusive profile of Mr. Holder, the agency took it as a signal that an inquiry was coming. Mr. Panetta felt blindsided and had several conversations with White House officials about the long-term damage he believed such an inquiry could do to the C.I.A. He said the C.I.A. had already taken disciplinary action against the officers who had committed the most egregious acts.
At the time, Mr. Panetta felt besieged on several fronts. Mr. Blair, the intelligence director, was pushing to appoint the senior intelligence officials in each country overseas, a traditional prerogative of the C.I.A.
And other administration officials complained when the C.I.A. sent documents about the detention program to the Senate Intelligence Committee without giving the White House time to consider whether there were any executive privilege issues.
The interagency debate grew heated enough that Mr. Emanuel summoned Mr. Panetta, Mr. Blair and other officials to the White House to set down rules for what should be provided to Congress. Mr. Panetta complained that he was being chastised for excessive openness after being criticized for excessive secrecy when he pushed to withhold details from the interrogation memos.
The various issues raised by the Bush-era interrogation and detention policies have caused other tensions within the Obama team. Mr. Emanuel and others have concluded that the White House mishandled the planning for the closing of the detention center at Guantánamo Bay, Cuba.
Some in the administration blamed Mr. Craig, the White House counsel, for not anticipating and managing the political reaction to the decisions on Guantánamo and other issues. After The Wall Street Journal suggested that Mr. Craig was on the way out, a White House official said Mr. Emanuel reassured Mr. Craig that it was nonsense, and Mr. Craig’s defenders said he had been handed a thankless task.
Throughout the summer, Mr. Holder indicated that he was still weighing whether to appoint a prosecutor. The C.I.A. dismissed that as empty posturing. To the agency, it was clear that Mr. Holder had already made up his mind and was planning to announce the investigation, as he did Monday even as the inspector general report was released.
Few cabinet officers are closer to Mr. Obama than Mr. Holder, and the issue has been awkward for the two. Aides said that they could not rule out that the two discussed the matter but said that there was never a formal White House meeting about it.Sensitive to the problems other administrations have had regarding politicizing the Justice Department, Mr. Obama left the decision to Mr. Holder, aides said.
By PETER BAKER