Acting Secretary of State Warren M. Christopher made clear yesterday that he plans to leave the State Department after helping Sen. Edmund S. Muskie (D-Maine) make a "smooth transition" into the secretary's job.

Christopher, who was passed over by President Carter when he chose a replacement for Cyrus R. Vance, told reporters after a meeting with Senate leaders: "I am encouraging Sen. Muskie to put together his own team, including his own deputy."

Imformed sources within the department amplified his remark by saying that Christopher, while believing that Muskie was a good choice, feels the new secretary should have a principal deputy, with whom he has the sort of working rapport and identity of views shared by Vance and Christopher during their 3-year tenure.

The sources said Christopher, who has not yet resigned, won't have a clear idea of his future plans until he confers with Muskie. But they said he is expected to tell Muskie it would not be wise to have two rivals for the same post working closely together, and the best course would be for him to leave in a few weeks after Muskie feels comfortable in control.

Christopher's intentions became known as several hundred foreign service officers and department employes crowded into the vast diplomatic lobby of the State Department late yesterday afternoon to bid farewell to Vance, who resigned because of his objection to last week's aborted attempt to rescue the American hostages in Iran.

Vance and his wife, Grace, seemed close to tears as they paused on a stairway landing over the lobby to receive a thundering ovation from the crowd below. Vance told those who had come:

"The qualities of the men and women of this department are unparalleled. It is with the greatest satisfaction that I know the tremendous dedication which I have seen will be continuing to help the president and my successor in the months and years ahead."

Referring to the 53 hostages in Iran, Vance said his "one great sorrow" in leaving "is the fact that a number of our colleagues are still unable to be here . . . My thoughts and my prayers will remain with them and with you in our efforts to bring them back safely just as much after I have left as they have been before."

Then, Vance led his wife along a cordoned-off pathway through the center of the crowd, pausing at each step to shake hands with well-wishers pressing forward from each side. With the crowd still cheering and applauding, they finally made their way through the huge glass doors of the department's main entrance and were whisked away in a waiting limousine.

Vance plans to go to the Caribbean island of Antigua to rest for a few days and to work on a speech he is scheduled to deliver June 4 at Harvard University.

Although Vance has refused to discuss in detail the reasons for his departure, department spokesman Hodding Carter said that, once the controversy surrounding his resignation calms, he plans to speak out concerning his views on the future course of U.S. foreign policy.

Interviewed on National Public Radio's "Communique" program, Hodding Carter said yesterday: "The secretary's time on this earth is not over."

In the meantime, department officials said the indications are that it will be at least two weeks, if not longer, before Muskie is in a position to take over the reins.

In addition to the need for Senate confirmation, Muskie is committed, as chairman of the Senate Budget Committee, to see through to completion work on a Senate resolution setting targets for federal spending in the 1981 fiscal year.

That is expected to take about two weeks, and the officials said the Senate Foreign Relations Committee probably won't begin confirmation hearings until then.

In the interim, the officials added, plans are being made for key department officers to begin briefing Muskie intensively on major foreign policy issues. But, as Hodding Carter noted, "given the senator's commitments, a lot of that might have to be done at night or on weekends."

Although sentiment within the department seems strongly in favor of the Muskie appointment, some officials questioned whether it would be wise to leave such a long gap before Muskie comes on board full time.

Christopher will be running the department's day-to-day affairs in the interim. But, given his lame duck status, some officials privately are concerned that the State Department will continue to lose influence over the Carter administration's policy direction in dealing with pressing situations such as the Iran crisis.

Implicit in this concern was fear that Muskie might arrive to find that leadership over administration foreign policy might have been vested decisively in other hands, particularly those of Carter's national security affairs adviser, Zbigniew Brzezinski.

Muskie, who was in Augusta, Maine, yesterday, seemed to be unconcerned about such fears. Asked about the possibility of finding himself in a power struggle with Brzezinski, he told a news conference there:

"I suspect the challenge here is not that one position or one personality is perferred; the challenge is to establish the role of secretary of state as the No. 1 voice.

"The president made it clear to me that's what he wants his secretary of state to do," Muskie said. "I took this job not to be second in foreign policy, but to be first."

Although Muskie's appointment continued to win widespread praise both at home and abroad yesterday, a dissenting view was expressed by Ronald Reagan, the frontrunning contender for the Republican presidential nomination.

Reagan, who was campaigning in Indiana, said he doubted Muskie "will have the kind of toughness that is needed in foreign-policymaking."