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For months, the CIA director, Leon Panetta, and the Director of National Intelligence (DNI), Adm. Dennis Blair (ret.), fought an intense and acrimonious turf battle over covert action oversight and access to White House officials. Last week, the two men agreed to a truce when they signed a classified memorandum brokered by the National Security Adviser, James Jones.

Through intermediaries, Panetta and Blair crossed swords over who should appoint senior intelligence representatives in foreign countries. Now, through interviews, new details are emerging about other, more sensitive conflicts between the two men and their agencies, including which agency is responsible for oversight of the CIA's controversial and classified Predator drone program.

According to the agreement, the details of which were confirmed by several officials, the CIA will retain responsibility for appointing senior intelligence representatives in foreign countries.  But other parts of the agreement seem to favor Blair. The Director of National Intelligence (DNI) will now be at the table whenever the CIA covert action programs are discussed at the White House. Also, Blair now has the authority to assess whether covert action programs fit with the nation's intelligence strategy.

Competition between the CIA, the nation's intelligence service, and the DNI, its new intelligence manager, has become fierce in the Obama administration. A victory for one side is seen by the other as a loss of power and authority. As part of the agreement, Blair and Panetta plan to meet weekly with National Security Adviser Jones. Face time with the president is preserved for both men. Blair, or his representative, briefs the president daily. Panetta has a standing meeting with the commander in chief at least one a week. In bureaucratic terms, both the CIA and the DNI need buy in. They need the White House to recognize their formal and informal authorities.

The conflict became public earlier this year, after the CIA protested when the Director of National Intelligence appointed a senior National Security Agency representative to be the DNI's representative in Kurdistan. Traditionally, the CIA's chief of station had served as the foreign nation's principal intelligence representative. But the NSA has a bigger footprint in Kurdistan, and the DNI decided that he would be better served by appointing an NSA officer to be his representative.  Then, the DNI and the CIA got into a dispute over the identity of the top intelligence officer for Pacific Command. Blair, former PACCOM commander in chief, wanted his own guy; Panetta had a different choice.

Blair assumed that the National Security Council would immediately settle the issue in his favor. After all, as he believed, the DNI structure couldn't work unless the White House acknowledged the supremacy of the office. Vice President Joe Biden was asked to mediate between Blair and Panetta. Biden held three meetings between the two with no appreciable progress. Last week, he decided in favor of Panetta.  This was a big victory for Panetta, who had lost several public rounds with the White House over the release of Bush-era torture memorandums  and the decision by the Justice Department to review interrogation files for potential prosecution.  Panetta opposed the document release on the grounds that they could hinder current intelligence collection and worried that interrogation prosecutions would dampen morale and were unnecessary. The National Clandestine Service -- still known to initiates as the "DO" -- or directorate of operations -- is a culture within a culture. So sacrosanct are its operational imperatives that Panetta might have faced an internal revolt had he not retain the appointment authority.

The conflict over covert action was even more sensitive. Since the CIA's establishment in 1947, its officers have had a direct line to the National Security Council. No cut-outs, no go-betweens.  Blair and his deputies believed that the CIA's National Clandestine Service was failing to provide a full picture of several of the agency's largest covert collection and special activity programs. In particular, the DNI would often find out about CIA-initiated drone strikes in Pakistan well after the fact. The CIA was conscientious about briefing the National Security Council, but did not bother to loop in the DNI.

That won't happen any longer. The CIA will keep its unfettered access to national security principals, and the DNI still doesn't have the authority to order covert action programs, but the White House is now requiring the CIA to fully brief the DNI on all covert action programs and will seek from the DNI regular assessments of whether any program fits in with the nation's intelligence strategy, which is set by Blair. Since Blair briefs Congress more often than Panetta does, it makes sense for Blair to know as much about covert action programs as CIA briefers would.

"The relationship between the White House and the CIA on covert action hasn't changed at all," a U.S. intelligence official sympathetic to the CIA's point of view said.  "That includes the direct line of command and communication between the President, who orders covert action, and the CIA, which carries it out. That's exactly how every president since Harry Truman has wanted it."

A third issue, regarding CIA attendance at meetings where non-CIA business is discussed,  has also been settled -- apparently in favor of the DNI.

Often, CIA officials would bring several representatives to N.S.C. meetings, even when they dealt with other, non-CIA intelligence activities. Blair complained that the CIA was over-represented at the meetings.  The CIA disagreed. But now, for any meeting that deals with non-CIA intelligence activities, Blair can decide whether a CIA or NSA person will represent the DNI. Of course, the White House can who they want, but the point, according to those familiar with the agreement, is that there is one intelligence community leader who decides who participates in high-level meetings.

According to an agreement, the DNI will be the primary intelligence community representative in all meetings -- but the CIA can still bring whoever it wants to them.

"On substance, things didn't go the DNI's way. He's talking about process and meetings, not action or results. If that's where he wants to find meaning or comfort, then fine," a source with knowledge of the agreement.

But another intelligence official said that the DNI was simply trying to institutionalize the roles and responsibilities as required by Congress. "The DNI is only acting to ensure that we don't repeat mistakes of the past where agencies worked independently and the nation suffered because we didn't have a comprehensive picture of what was going on," he said.

The White House tried to put the best spin on the feud and the resulting truce. "[National Security Adviser James]  Jones, Director [Dennis] Blair, and Director [Leon] Panetta clarified and reached agreement on an important provision of the 2004 Intelligence Reform Act," the NSC's chief of staff said in a statement. "They also reaffirmed the importance of intelligence reform and that the intelligence community needs a strong and unified leader to ensure maximum cooperation. It is a good agreement that advances the country's interests and ensures that we are continuing to work together as a team."