A federal appeals court in Richmond yesterday overturned the 1979 conviction of Dr. Murdock Head, the former Airlie Foundation director who was contesting a three-year prison sentence for allegedly conspiring to bribe government officials.

A three-member panel of the 4th U.S. Circuit Court of Appeals ordered a new trial for Head, 56, on grounds that trial Judge Oren R. Lewis failed to instruct the jury about the statute of limitations governing Head's alleged payments to former Democratic Reps. Daniel J. Flood and Otto F. Passman.

Federal prosecutors refused to say yesterday whether they would seek to retry Head, the dapper George Washington University professor and former chief of the University's department of medical and public affairs.

Head, in a two-page statement, blasted the government lawyers and their handling of his case, which he called "a legal can of worms" handled by "rogue prosecutors" who brought the "relentless and punitive machinery of an unbridled judicial bureaucracy" to bear against him and the organizations he controlled.

Calling on the Reagan administration to take "a fresh look at the origins of this case, the questionable methods . . . and overall focus and goals of the Department of Justice," Head contended he had been the victim of "the excesses of young, ambitious prosecutors who have become a law unto themselves."

Head's attorney, Frank W. Dunham, said he believed federal prosecutors would seek a new trial, but added, "I could see the new administration saying . . . it might be counter-productive and overly expensive of public funds."

A trim, athletic man who holds advanced degrees in law, medicine and dentistry. Head was portrayed by prosecutors at his trial as the "self-anointed major-domo of the entire Airlie complex." The sprawling, tax-exempt foundation, which bills its wooded conference center as an "island of thought," is nestled in the Virginia foothills of the Blue Ridge Mountains 50 miles west of Washington.

Head's conviction followed testimony that he conspired to arrange bribes totaling $49,000 to Flood and Passman in exchange for their help in obtaining lucrative federal contracts and grants to bolster the foundation, which Head founded in 1960.

It was reported later, however, that the jury did not believe Head had bribed the congressmen and convicted him instead on a separate issue in the trial: that he allegedly conspired to arrange an improper $11,000 loan to a former Internal Revenue Service agent in return for favorable tax treatment for Airlie and Head's other enterprises.

Head's 1979 trial was marked by frequent, bitter exchanges between the lawyers and Judge Lewis, a crusty, controversial 78-year-old jurist who frequently chided attorneys for both sides and once accused a prosecutor of "demeaning the bar."

Before the start of the trial, prosecutors unsuccessfully urged the appeals court to remove Lewis as the presiding judge, arguing that he had displayed an "angry attitude" and "appearance of bias" against the prosecution.

During the course of the trial Lewis dismissed eight of 13 counts on which Head had been indicted by a grand jury, saying that in some cases the statute of limitations had expired.

In his appeal, Head argued the jury should have been told a conviction could be returned only if any alleged conspiracy was found to have continued after July 1974.

That issue was addressed yesterday by the appellate panel in its 20-page ruling. "We simply have no way of knowing whether Head was convicted for an offense barred by limitations. We decline to engage in speculation of this sort in determining guilt in a criminal case."

In attempting to prove its allegations that Head had sought to bribe Flood and Passman, prosecutors relied heavily on testimony by Stephen B. Elko, Flood's former assistant, who was on parole from a two-year prison sentence for perjury in connection with an unrelated case.

Elko, who testified under a grant of immunity from further prosecution, described a series of meetings at Airlie Headquarters near Warrenton during which he said Head allegedly gave him $49,000 in payoffs intended for passman, whom he called "The Priest" and Flood, whom he called "The Mustache." Elko said Flood used facial tissue when picking up the cash to avoid leaving fingerprints on it.

In his statement yesterday, Head called Elko a "convicted perjurer" whose testimony was "force-fed" by John Dowd, a former Justice Department official who led the federal strike force team that prosecuted Flood.

Head said Dowd, now an attorney in private practice in Washington, sought to "vilify Daniel Flood and others" and in turn "brought the vast resources of the FBI and IRS to bear against any and all persons," including Head. Flood pleaded guilty last year to a misdemeanor charge of conspiring to solicit illegal campaign contributions and was placed on probation for one year.

"John Dowd is long since out of government, but the bill of goods he sold his successors lives on," Head wrote, calling his case "an assault now in its fourth year."

Dowd declined comment yesterday on Head's statement.