Hours after the two top clandestine service officers at the CIA resigned yesterday, Director Porter J. Goss asked employees to remain loyal to the agency and rebutted allegations that he had a partisan agenda.

"We provide the intelligence as we see it and let the facts alone speak to the policymakers," Goss wrote in an internal e-mail to CIA employees, according to two people who read it to The Washington Post. Goss told them to expect "a series of changes" in the days and weeks ahead, "in the organization, personnel" and mission of the agency.

The e-mail was the first communication from Goss to the wider CIA audience since controversies arose over senior aides he has appointed.

Goss has said he believes the CIA's clandestine service is dysfunctional and needs changes. His critics say the director, a former CIA case officer and Republican chairman of the House intelligence committee, is purging the agency of career officers whom he incorrectly perceives as critical of Bush administration policies.

In addition, Goss has over the last month put in charge several former Hill staff members who are not well regarded by senior officials because they lack managerial and operational experience, and are believed to have treated career officers disrespectfully.

This is not the first time a new director's personnel changes have put the agency in turmoil, but the criticism of the Goss team's actions is the first to raise questions of partisanship.

Sen. John McCain (R-Ariz.) said yesterday that Goss and some White House officials were concerned that unauthorized disclosures of information by the CIA during the election campaign "were intended to damage the president," and he accused a "rogue" element within the agency of carrying them out.

Rep. Jane Harman (Calif.), ranking Democrat on the House intelligence committee, yesterday accused Goss's aides of having partisan motives. Targeting officials in the clandestine service, whose job is to manage CIA operations around the world, for leaks of a prewar National Intelligence Estimate on Iraq's weapons of mass destruction was "totally misguided," she said.

The two resignations yesterday, of Deputy Director of Operations Stephen R. Kappes and his deputy, Michael Sulick, will "undermine the morale of the workforce that had undergone a renaissance since the failures of 9/11," she said.

Goss yesterday named the current director of the counterterrorism center to replace Kappes. His name is being withheld by The Post because he is still undercover. He is a 28-year employee with lengthy experience in Latin America and was the chief of station in Mexico, according to several former CIA officers.

"There will be no gap in our operations fighting the global war on terror, nor in any of our other vital activities," Goss said in a separate statement released yesterday.

Kappes is a widely respected officer who helped persuade Libyan leader Moammar Gaddafi to renounce weapons of mass destruction this year. Sulick, whose career includes assignments in South America, the former Soviet Union and Eastern Europe, headed the agency's counterintelligence center until becoming Kappes's deputy. Both are highly regarded by clandestine service colleagues, said 10 former CIA officials who worked with them.

Also last week, the agency's deputy director, John E. McLaughlin, retired.

The personnel moves follow a series of confrontations between Goss's new chief of staff, Patrick Murray, and senior operations staff members.

Last week, Murray demanded that Kappes fire Sulick after Sulick criticized Murray at a meeting, according to several current and former CIA officials. Kappes declined and offered his resignation. McLaughlin announced his retirement, and several other senior operations officers have threatened to resign, the current and former officials said.

Goss's internal e-mail also attempted to calm fears that Murray has wide-ranging authority and that Goss intends to dilute the power of the directorate of operations. Last week, Murray told managers that the directorate will lose its key role in appointing station chiefs and regional division chiefs, according to several current and former employees.

"The division deputy directors," Goss's statement said, "would have complete responsibility for managing their components." Murray "organizes and manages the duties and priorities of my staff."

A CIA spokesman declined to comment.

McCain also cited a leak of information about Michael V. Kostiw, Goss's initial choice for the number three position at the agency, as evidence of partisan opposition to the new director. That leak, concerning a 20-year-old shoplifting incident, resulted in Kostiw's withdrawal from consideration for that job. He is now a special assistant to Goss.

"The information was leaked before he even got there," McCain said.

Sen. John D. Rockefeller IV (W.Va.), ranking Democrat on the Senate Select Committee on Intelligence, said that he had expected changes at the CIA based on past failures but that Goss "must provide some explanation for this rash of departures among senior officials."

In 1977, when retired admiral Stansfield Turner was named CIA director by President Jimmy Carter, he brought to agency headquarters what one former CIA official described as "a Navy boarding party armed with sabers." Turner's aides fired several senior clandestine officials, and although the actions were resented they were never believed to have had partisan motives.