The deputy director of the CIA resigned yesterday after a series of confrontations over the past week between senior operations officials and CIA Director Porter J. Goss's new chief of staff that have left the agency in turmoil, according to several current and former CIA officials.

John E. McLaughlin, a 32-year CIA veteran who was acting director for two months this summer until Goss took over, resigned after warning Goss that his top aide, former Capitol Hill staff member Patrick Murray, was treating senior officials disrespectfully and risked widespread resignations, the officials said.

Yesterday, the agency official who oversees foreign operations, Deputy Director of Operations Stephen R. Kappes, tendered his resignation after a confrontation with Murray. Goss and the White House pleaded with Kappes to reconsider and he agreed to delay his decision until Monday, the officials said.

Several other senior clandestine service officers are threatening to leave, current and former agency officials said.

The disruption comes as the CIA is trying to stay abreast of a worldwide terrorist threat from al Qaeda, a growing insurgency in Iraq, the return of the Taliban in Afghanistan and congressional proposals to reorganize the intelligence agencies. The agency also has been criticized for not preventing the Sept. 11, 2001, attacks and not accurately assessing Saddam Hussein's ability to produce weapons of mass destruction.

"It's the worst roiling I've ever heard of," said one former senior official with knowledge of the events. "There's confusion throughout the ranks and an extraordinary loss of morale and incentive."

Current and retired senior managers have criticized Goss, former chairman of the House intelligence committee, for not interacting with senior managers and for giving Murray too much authority over day-to-day operations. Murray was Goss's chief of staff on the intelligence committee.

Transitions between CIA directors are often unsettling for career officers. Goss's arrival has been especially tense because he brought with him four former members of the intelligence committee known widely on the Hill and within the agency for their abrasive management style and for their criticism of the agency's clandestine services in a committee report.

Three are former mid-level CIA officials who left the agency disgruntled, according to former colleagues. The fourth, Murray, who also worked at the Justice Department, has a reputation for being highly partisan. When senior managers have gone to Goss to complain about his staff actions, one CIA officer said, Goss has told them: "Talk to my chief of staff. I don't do personnel."

The overall effect, said one former senior CIA official, who has kept up his contacts in the Directorate of Operations, "is that Goss doesn't seem engaged at all."

If other senior clandestine officers leave, said one former officer who maintains contacts within the Langley headquarters, "the middle-level people who move up may eventually work out, but meanwhile the level of experience and competence will go down."

The CIA declined to comment on the issues raised by the current and former officials, who spoke on the condition of anonymity. A CIA spokesman said McLaughlin's retirement "was a long-planned personal decision taken at a natural transition point in the administration and not connected to any other factors."

McLaughlin issued a statement that said: "I have come to the purely personal decision that it is time to move on to other endeavors."

Goss, too, issued a statement, which applauded McLaughlin's "outstanding service."

"On a personal note," the statement continued, "I want to thank John for the kindness he has shown me as Director of Central Intelligence."

In addition to bringing in his former aides from the Hill, Goss plans to dilute the authority of the Directorate of Operations by removing the director as the central figure in appointing country station chiefs overseas and regional division chiefs at headquarters.

"I definitely think all this is disrupting people's work," one agency official said. "Everyone is waiting for the centipede to drop all his shoes."

Associates said McLaughlin was disappointed by Goss's management style and was particularly disheartened by a series of recent confrontations between Murray and senior leaders.

In one of those confrontations, on Nov. 5, Murray raised the issue of leaks with the associate deputy director of counterintelligence. Referring to previous media leaks regarding personnel, he said that if anything in the newly appointed executive director's personnel file made it into the media, the counterintelligence official "would be held responsible," according to one agency official and two former colleagues with knowledge of the conversation.

All three sources gave the following account:

The associate deputy director of counterintelligence, a highly respected case officer whose name is being withheld because she is undercover, told Michael Sulick, the associate deputy director of operations, about the threat. Sulick told his superior, Kappes, and both sought a meeting with Goss to complain.

Goss, Murray, Kappes and Sulick met to discuss the matter. After Goss left, Sulick "got in Murray's space," according to one of his associates whose account was corroborated by another. Murray then demanded that Kappes fire Sulick. Kappes refused, and told Goss that he would resign. Goss and other White House officials appealed to Kappes to delay his decision until Monday.

Goss, a former CIA case officer and Republican legislator from Florida, promised during his confirmation hearing to set aside partisan politics and work to strengthen the CIA clandestine service. But current and former officials have said that his plans have been unclear to the senior clandestine service officials who would be responsible for carrying them out. In addition, they have been concerned by the backgrounds of the senior staff Goss has hired.

Michael V. Kostiw, who was Goss's first choice for executive director -- the agency's third-ranking official -- withdrew his name after The Washington Post reported that he had left the agency 20 years ago after having been arrested for stealing a package of bacon.

More generally, Goss's aides arrived at the CIA with harsh views of the clandestine service. Their views were laid out in a House intelligence committee report in June. "There is a dysfunctional denial of any need for corrective action," the report said. The clandestine service suffers from "misallocation and redirection of resources, poor prioritization of objectives, micromanagement of field operations and a continued political aversion to operational risk."

The report was drafted primarily by Jay Jakub, whom Goss appointed to the newly created position of special assistant for operations and analysis.

The House report's critique brought on a tough response from then-CIA Director George J. Tenet and led to a near-breakdown in relations between the agency and the panel staff. It was repeatedly noted by present and past clandestine officers that Jakub had a limited career at the agency, first as an analyst and later as a case officer.

"He never distinguished himself before he left," a former boss said.

CIA Director Porter J. Goss has been criticized for not interacting with his senior managers. In resigning, John E. McLaughlin warned that Goss's top aide could be driving others to leave. Goss vowed at his confirmation hearing to bolster the clandestine service.