The pending appointment of General Michael Hayden as director of the Central Intelligence Agency will pave the way for the agency’s emasculation and for the Pentagon to assume full authority over paramilitary operations.

A senior intelligence community official yesterday said the director of national intelligence, John Negroponte, has indicated “he is willing to give up covert operations to the Pentagon.”

The source also pointed out that the Pentagon has requested increased budget authority to prepare for the acquisition of the CIA’s targeted military operations. The intelligence overhaul of 2004 envisioned that they would remain under the purview of the CIA.

The authority to commission and plan these secret military operations has been a point of contention since 2004 when Congress and the White House began reorganizing the intelligence community.

The proposed change would give the Pentagon unfettered authority to plan and conduct these operations without consulting an intelligence bureaucracy its civilian leaders have deemed hostile to the president’s war policy.

Already, General Hayden’s appointment has provoked opposition from members of Congress from both parties, including some of the president’s allies. In an interview yesterday with The New York Sun, the chairman of the House Permanent Select Committee on Intelligence, Peter Hoekstra, a Republican from Michigan, said had he known Porter Goss was leaving his position as head of the CIA, he would have included language in the intelligence reauthorization bill prohibiting an active member of the military from becoming the CIA director.

“Putting a military person into this role is just a bad idea,” Mr. Hoekstra said. “I think you will have the CIA folks in D.C. and the CIA folks around the world see this as the last straw. I am not sure you will see resignations. But people who have chosen the CIA as a career, I don’t think ever envisioned it being run by a general.”

Mr. Hoekstra also said he thought the fact that Mr. Goss was stepping down at this moment – after firing an analyst accused of leaking to the press, Mary McCarthy – sent the wrong signal to those in the CIA who oppose the president’s policies.

“Two weeks after Porter takes one of the biggest steps to send a clear signal around the agency on leaks, he loses his job. I don’t know how people will read this.

“Some people might say insubordination at the CIA is going to be tolerated. This is the last major decision which I thought was crucial to the agency. There had been a lot of people knifing Porter in the back. He was sent in as an agent of change. Some people over there might believe they won.”

Mr. Hoekstra’s predecessor at the House Intelligence Committee, Porter Goss, stepped down from his perch at Langley on Friday amid rumors that his aide and CIA no. 3, Kyle Foggo, was connected to a corruption scandal involving the former California Republican congressman, Randy Cunningham. Over the weekend, however, the CIA denied there was any connection between the Justice Department investigation and Mr. Goss’s departure.

Mr. Goss’s replacement, General Hayden, who currently serves as Mr. Negroponte’s deputy for intelligence, is a four star Air Force general and the former chief of the National Security Agency, the government’s center for the collection and analysis of signal and technical intelligence.

He was in charge of the NSA when the president authorized the tapping of overseas phone numbers found on cell phones captured on suspected Al Qaeda terrorists.

Yesterday some lawmakers said his role in overseeing those wiretaps may make his confirmation in the Senate less likely. On Fox News Sunday, the chairman of the Senate Judiciary Committee, Arlen Specter, a Republican from Pennsylvania, said, “There is no doubt there’s an enormous threat from terrorism, but the president does not have a blank check. Now, with General Hayden up for confirmation, this will give us an opportunity to try to find out.”

Mr. Specter’s counterpart at the Senate Select Committee on Intelligence, Pat Roberts, a Republican from Kansas would not say on CNN yesterday whether General Hayden had his vote for confirmation.

Meanwhile, Senator Chambliss, a Republican of Georgia and member of the Senate Intelligence Committee, told ABC’s “This Week” program, “I too have a little bit of concern, frankly, about military personnel running the CIA.”

One factor driving that concern is that the Congressional authors of the 2004 intelligence reform fought the Pentagon to keep oversight and authority over covert military operations in the directorate of national intelligence and CIA.

But the senior intelligence community official yesterday said he expected almost everything except for the human intelligence collection role of the CIA to be removed from the agency. This source said that Mr. Negroponte “is going to strip analysis, strip out covert operation, science, and technology.”

The founder of the CIA’s Counterterrorism Center, Duane Clarridge yesterday said he also predicted his old place of employment would be significantly diminished.

“The CIA as an institution will become the directorate of operations with some ancillary components,” he said. “In the end, what you’ve got, where you’re headed, even though these people may not understand it yet, is a directorate of operations writ large, a la M16.”

In his one and a half year tenure as the director of the CIA, Mr. Goss attempted to reform an agency whose former members have aggressively attacked the president’s decision to go to war in Iraq. One of his first acts as director was to remind gathered employees at headquarters that the information they trafficked was secret and that they worked for the president.

Under his tenure, one director, two deputy directors and 13 department heads and station chiefs left the agency’s directorate of operations. Last month, a CIA analyst, Mary McCarthy, stepped down from her job allegedly for discussing classified information with Washington Post reporter Dana Priest.

Mr. Goss himself testified before Congress earlier this year that he looked forward to when the Justice Department began interviewing reporters about their sources on the NSA wire tapping story, broken by the New York Times in December.

The former chairman of the Defense Policy Board, Richard Perle, said he does not expect the next CIA director to have better luck with leakers. “The crackdown on leaking will make people more careful,” he said, adding that leakers at the CIA will just get information out through former CIA officers who are cleared to get the information.

“Until they get serious about leaks, which is to put people on polygraphs after every major leak, it is going to go on. Remember, this is an institution that is steeped in covert operations and misinformation. We train people to lie and we are shocked when they lie.”