Two months after touching off the Central Intelligence Agency's tumultuous reorganization effort with a curtly worded dismissal notice to 212 senior members of the agency's clandestine operations branch, the CIA's top operations official has been notified that he is also being replaced.

A CIA spokesman confirmed yesterday that William W. Wells, the CIA's deputy director for operations, will retire at the end of December. Knowledgable sources said Wells and his top deputy. Theodore Shackley, were dismissed from their operations posts shortly before Christmas after a falling out with CIA Director Stansfield Turner.

Turner announced Wells' retirement at a meeting Tuesday of senior CIA officials at headquarters in Langley, Va. The CIA's spokesman yesterday denied that Shackley had been fired by Turner. "As far as I know he's staying but we don't yet know in what capacity," the spokesman said.

The removal of the two senior operations officials was seen by some top CIA officials as part of Turner's announced top-to-bottom housecleaning of the cladestine arm and an attempt to break up remnants of the "old boy" network of senior operations agents in favor of more science and technologically oriented intelligence-gathering.

Turner has formally announced that he plans to cut the operations directorate, which has been sharply criticized in recent years for its covert foreign activities, by more than 800 persons, including many of the directorate's most senior officials.

The CIA's spokesman said Wells will be replaced by John N. McMahon, the current acting deputy to Turner for intelligence. McMahon is a 26-year CIA veteran whose specialty in the past has been in the area of science and technology.

Wells and Shackley were generally considered two of the CIA's top clandestine operators. Wells was a station chief for the intelligence agency in Tokyo and Hong Kong and gained the nicknamed "Wild Willy" among some of his colleagues. He also headed the CIA's European operation division. Shackley directed the CIA's secret war in Loas and was actively involved in CIA operations during the Cuban missile crisis and in Berlin.

Wells' dismissal is particularly ironic since he signed th controversial two-sentence memo sent Oct. 31 to senior operations officials notifying them of their firing.

His memo said: "This is to inform you of my intend to recommend to the Director of Personnel your separation in order to achieve the reduction in Operations Directorate strength ordered by the DCI [Director of Central Intelligence]. I or my designee will first review your case with the Director of Personnel or his designee."

A number of those who received the hand-delivered memos have angrily broken the CIA's traditional cloak of silence and complained - although anonymously - about the cold tone of the dismissal.

Several of those who received the notes said yesterday that it is possible Wells may have drawn them up and sent them out without first clearing their tone and language with Turner.

But one high-ranking CIA official on the dismissal list said, "Turner went to Harvard Business School. He knows that he's the one who's responsible for those memos no matter who actually sent them out."

Under the provisions of the 1947 National Security Act, Turner, as CIA director, has the authority to fire anyone on the CIA payroll without review or appeal.

Some CIA officials, who asked yesterday not to be identified, said they were still unclear as to whether the shift at the top of the operations branch signified a full-scale downgrading of its traditional cloak-and-dagger method of gathering intelligence.

Some people are going to read this as, bring an outsider into the operations directorate when there are people already there who were capable of taking the job," said a veteran CIA clandestine official.

On the other hand, the CIA official and others in the intelligence agency noted that so much bitterness had been raised over Wells' dismissal memos that his effectiveness may have been wiped out as operations director.

According to another CIA official, Shackley and Turner had several angry confrontations over management policy recently.After one such flareups two weeks ago, Shackley stalked out of Turner's seventh-floor office and Shackley's secretary began callig the CIA's logistics arm to prepare for the removal of secured communications equipment from Shackley's home.