WASHINGTON » With the appointment of a prosecutor to investigate detainee abuses, long-simmering conflicts between the CIA and the Justice Department burst into plain view this week, threatening relations between two critical players on President Barck 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 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, CIA Director Leon Panetta tried to head off the investigation, administration officials said. He sent the CIA's top lawyer, Stephen W. Preston, to Justice to persuade aides to Attorney General Eric Holder to abandon any plans for an inquiry.

Preston presented what was, in effect, a closing argument in defense of the CIA, 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 CIA pressure and the stated desire of the White House not to dwell on the past, 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, Panetta phoned Holder, according to people familiar with the call. In the conversation, which lasted less than a minute, the CIA director told the attorney general that the agency would cooperate but expressed his displeasure and swore mildly, if only once.

Holder and Panetta are each confronting difficult balancing acts. 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.

Panetta, who is also new to his job and lacks a background in intelligence, must carry out White House's orders to make a clean break with some of the Bush administration's intelligence policies, including ending the CIA's harsh interrogations. At the same time he must soothe frayed nerves at the CIA.

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 agency's viewpoints in robust discussions, as they should. “;Leon's representing his institutional building,”; Emanuel said. “;Eric's representing his institutional responsibilities.”;

While top CIA officials are angry at the Justice Department, 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 Panetta and 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 ACLU lawsuit, the Justice Department prepared to release legal opinions written by its lawyers during the Bush administration authorizing the CIA to use brutal interrogation techniques.

Obama disavowed the harsh methods, like waterboarding and wall-slamming, but the legal opinions were filled with embarrassing details about the CIA's aggressive approach. Panetta sought to heavily edit the memos before releasing them but was overruled when Obama sided with Holder, who wanted more detailed disclosures, the officials said.

Though he lost on the memos, 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, CIA officers felt reassured by Emanuel's comments on ABC News, in which he said that 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 Emanuel had meant was that CIA officers who followed interrogation guidelines were safe from prosecution.

Holder took 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 CIA custody in Iraq and Afghanistan.

Still, it came as a shock to the CIA when Newsweek reported in July that Holder was leaning toward an investigation. Given that the information was contained in an exclusive profile of Holder, the agency took it as a signal that an inquiry was coming. 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 CIA. He said the CIA had already taken disciplinary action against the officers who had committed the most egregious acts.

At the time, Panetta felt besieged on several fronts. Blair, the intelligence director, was pushing to appoint the senior intelligence officials in each country overseas, a traditional prerogative of the CIA.

And other administration officials complained when the CIA 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 Emanuel summoned Panetta, Blair and other officials to the White House to set down rules for what should be provided to Congress. Panetta complained that he was being chastised for excessive openness after being reprimanded 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. Emanuel and others have concluded that the White House mishandled the planning for the closing of the detention center at Guantanamo Bay, Cuba.

Some in the administration blamed Craig, the White House counsel, for not anticipating and managing the political reaction to the decisions on Guant anamo and other issues. After The Wall Street Journal suggested that Craig was on the way out, a White House official said Emanuel reassured Craig that it was nonsense, and Craig's defenders said he had been handed a thankless task.

Throughout the summer, Holder indicated that he was still weighing whether to appoint a prosecutor. The CIA dismissed that as empty posturing. To the agency, it was clear that 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 Obama than 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, Obama left the decision to Holder, aides said.