Tim Kraft, President Carter's national campaign manager, stepped down from his job yesterday following published reports that a special prosecutor has been named to investigate allegations he used cocaine while a member of the president's staff.

"Although I am completely innocent of the charges, I find myself in a very difficult situation and facing a difficult decision," Kraft said in a prepared statement.

"I have not worked hard for President Carter for the past six years just to become a subject of political controversy in the final six weeks of his reelection campaign . . . Therefore, I have concluded that I can best serve the president and avoid political explotation of the false charges against me by taking a leave of absence from the campaign."

Kraft's statement said he had learned last month that the FBI was conducting an investigation into allegations that he had used cocaine on two occasions within the last few years. He said that, in a voluntary interview with the FBI, he had categorically denied those accusations.

Kraft was the Carter campaign's expert in field operations. There was no immediate indication last night whether the allegations that have been raised concerning him will become an item of controversy in the last month and a half of the campaign.

The allegations apparently grew out of an investigation by special prosecutor Arthur H. Christy into similar accusations against Hamilton Jordan, then White House chief of staff and now a top Carter strategist.

Jordan was accused of sniffing cocaine during a 1978 visit to the New York City discotheque, Studio 54.

The charge was made by Steve Rubell and Ian Schrager, the discotheque's owners, who were then awaiting trial on tax evasion charges unrelated to drug dealing.

The New York Times and CBS News reported earlier yesterday, quoting sources familiar with that investigation,that a White House aid told a federal grand jury in the Jordan case that he had observed Kraft use cocaine in New Orleans in 19779 The sources did not identify the witness.

That grand jury found insufficient evidence to support the allegations against Jordan, who remained in his job throughout the investigation.

In his statement, Kraft, who was Carter's appointments secretary in 1977, said he had been told last week by the Justice Department that the investigation "had been referred to the court for the appointment of a special prosecutor," and "I have now learned from press reports" that a special prosecutor has been appointed.

The Times and CBS reported that a panel of three federal judges had named Gerald J. Gallinghouse, a 60-year-old New Orleans lawyer and former U.S. attorney from that city, to serve as special prosecutor.

Gallinghouse, a Republican, indirectly confirmed those reports yesterday in an interview.

"My friend, I regret very much that there's been publicity on this matter -- obviously emanating from New York. I guess the first thing I'm going to have to do is to try to plug the leaks up there," he said.

Gallinghouse refused further comment.

Under the Ethics in Government Act of 1978, the U.S. attorney general is required to order a preliminary investigation into all allegations of federal criminal misconduct against ranking federal government or campaign officials.

Unless the preliminary investigation proves the charges baseless, the attorney general is obligated to seek the appointment of a special prosecutor.

Attorney General Benjamin R. Civiletti last year asked the three-judge panel to appoint the special prosecutor in the inquiry that eventually cleared Jordan.

Robert S. Strauss, Carter campaign chairman, said yesterday that he deeply regretted "that the Carter-Mondale campaign will be deprived of the services of a fine young man who has categorically denied the allegations against him."

Strauss said in a statement that he had no doubt Kraft would be vindicated and "I trust that everyone will understand that the appointment of a special prosecutor . . . is in no way an indication of guilt or wrongdoing."

Kraft is being represented by Washington lawyer Thomas C. Green, who was quoted as saying yesterday that he was "dismayed [to] have to find out the name of the special prosecutor from The New York Times and not the Department of Justice."

Green was unavailable for further comment.

White House and Justice Department officials also declined comment yesterday.

Yesterday afternoon, at the Carter-Mondale headquarters, Kraft conferred with Green, campaign counsel Tim Smith and White House press secretary Jody Powell. At that session, according to a campaign official, Kraft's statement announcing his decision to take a leave was drafted. Kraft also spoke by telephone with Strauss.

Kraft also conferred by telephone with a number of the Carter cammpaign state coordinators and the four deputy campaign managers whom he had chosen.

One campaign official, who asked not to be identified, said that it was unlikely that Kraft's departure would have a significant impact on the daily operation of the campaign. "Because of what Tim did before he left," the official said, "by calling all of the state coordinators and the deputy campaign managers whom he had handpicked and trained, I don't think there will be many problems from a nuts-and-bolts standpoint. I think they'll continue to do their jobs."

Asked whether it was likely that the allegations surrounding Kraft would become a campaign controversy, the official said, "The reason he took his leave of absence was to avoid the political exploitation of it . . . "

Later yesterday, several top Carter officials attended what was described as the regular Sunday meeting on campaign scheduling at the headquarters. Officials who were present denied the Kraft matter was discussed.

A campaign official said no decision was reached on whether anyone would be given Kraft's title of national campaign manager during his leave of absence.

Kraft, a 39-year-old Indiana native who was instrumental in organizing Carter's 1976 campaign, had served as the president's appointments secretary until Aug. 10, 1979, when he was asked to manage the Carter reelection campaign.

The appointment, along with several other shifts in the White House staff, signaled stepped-up preparation for the 1980 presidential race.

Kraft replaced Evan Dobelle, who had been the campaign's top executive for eight months, but who was shifted to fund-raising when Kraft came on board.

Kraft is a graduate of Dartmouth College and a former Peace Corps volunteer.