In a statement Friday, McLaughlin, the CIA's deputy director and 32-year agency veteran, called his departure a "purely personal decision" and said it was time to move on to other endeavors.
But former intelligence officials in touch with current agency personnel say there has been turmoil in recent weeks as new CIA Director Porter Goss tried to make changes and get settled in.
The Washington Post notes in its Saturday editions that, "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."
The newspaper quotes a former senior official with knowledge of the events as saying, "It's the worst roiling I've ever heard of. There's confusion throughout the ranks and an extraordinary loss of morale and incentive."
Goss, a Florida Republican who formerly chaired the House Intelligence Committee, brought four of his congressional aides with him to the CIA's 7th floor executive offices shortly after he took over in September.
But tension began before he arrived.
Officials as senior as former CIA Director George Tenet fumed at legislation approved by Goss' committee and the full House that said the CIA's Directorate of Operations "needs fixing." The bill warned that without changes, the clandestine unit - the agency's most famous division - could become a "stilted bureaucracy incapable of even the slightest bit of success."
Now, moves made by Goss and his aides are believed to be riling current personnel. The Post reported Saturday that Deputy Director of Operations Stephen Kappes turned in his resignation Friday following a tense meeting at CIA headquarters in suburban Virginia.
Goss and White House officials asked Kappes to reconsider his decision over the weekend, the newspaper said. Other officials are also considering leaving.
An intelligence official reached late Friday declined to comment.
McLaughlin temporarily took over the CIA in July when Tenet retired, also citing personal reasons.
McLaughlin's ascension put him in line to field criticism from two reports highly critical of U.S. intelligence operations, the Sept. 11 Commission report and the Senate's investigation into the flawed prewar intelligence on Iraq.
President Bush decided in August to nominate a permanent replacement for Tenet and tapped Goss, who was a CIA operative during the 1960s.
Officials painted McLaughlin's decision to retire from government as a natural one: A CIA official said McLaughlin thought the period of government transition after the election was a "logical time to move on." McLaughlin plans to take time off while considering opportunities in the private sector, said the official, who spoke on condition of anonymity.
Since 1972, McLaughlin has advanced within the agency to become a part of its senior leadership. He was an analyst for European and Russian issues before rising to deputy director for intelligence in 1997. By 2000, he had become Tenet's right hand, as deputy director of central intelligence.
When Tenet announced resigned in July, McLaughlin temporarily headed the agency for nearly three months.
McLaughlin, 62, called "Merlin" by some of his colleagues, was known for pulling off impromptu magic tricks, like turning a dollar bill into other denominations.