Two Justice Department prosecutors charged yesterday that a decision to withhold commendation awards from them because they had questioned a superior's handling of a criminal case was a deliberate attempt to stifle dissent and intimidate department employes.

The attorneys, Michael A. Lubin and George J. Mendelson, said their feeling was heightened by the disclosure that a third attorney scheduled to receive an award at the department's ceremony yesterday also was stripped of the honor because he criticized Attorney General William French Smith.

Department spokesman Thomas DeCair said that the third lawyer, Michael H. Sussman, who left the civil rights division recently, was refused a special commendation award because he had written "an intemperate, unprofessional memo" questioning the legal underpinning of a speech in which Smith denounced the use of busing and quotas in civil rights cases.

"We don't give awards to people who act unprofessionally," DeCair said, speaking of all three attorneys. DeCair volunteered the information about Sussman but denied that he or anyone in the department was trying to "send a message" intended to stifle dissent.

Lubin and Mendelson had criticized Associate Attorney General Rudolph W. Giuliani for holding a May 14 meeting with the general counsel of McDonnell Douglas Corp., without their knowledge, to discuss the over-seas-bribery case pending against the firm.

Giuliani denied any impropriety, saying he hadn't been aware of the criminal charges until they were raised at the meeting. He also attacked Lubin and Mendelson for displaying "a disrespect for the facts and an immature petulance."

The pair was told Wednesday that their awards would be held "in abeyance" until the issues arising from their critical June 18 letter to Giuliani were resolved. They, in turn, wrote D. Lowell Jensen, head of the criminal division, contending that withholding the awards is a reprisal prohibited by the whistleblower protections of the civil service reform act.

Lubin, 32, and Mendelson, 35, attended the department's ceremony yesterday even though they didn't receive their awards. Afterward, each read a statement to reporters.

Lubin criticized the withholding as "petty and vindictive . . . an indecent action that does not speak well of the department." It was a reminder of the "enemies lists" in the Nixon administration, he added.

"I am angered by the personal attacks, but more importantly, I am disgusted and saddened by what I believe is a deliberate attempt to send a message to anyone in the Department of Justice who dares to speak, who dares to criticize impropriety at high levels," Mendelson said. He added that he hoped other department attorneys wouldn't be "intimidated by any threat of reprisal for speaking out to correct abuses."

The department's office of professional responsibility (OPR) is reviewing Giuliani's conduct because regulations require that lawyers' actions give not even the "appearance" of impropriety. DeCair sid Wednesday that Lubin and Mendelson's conduct also were being reviewed by the internal investigators, but corrected that statement yesterday.Jensen is withholding the awards while he reviews their conduct.

Richard M. Rogers, who is handling the OPR review, said it also could include a look at Lubin and Mendelson's reprisal charges.

Sussman's criticism of Smith came in a memo he wrote shortly before leaving the department to join the legal staff of the NAACP. He said Smith's disavowal of busing and quotas as desegregation remedies gave comfort to opponents of an integrated America. DeCair said Sussman did everything but call Smith a racist in the memo.

Sussman also discussed his misgivings about department civil rights policies with The Washington Post. "That was not the most appropriate means of communicating," DeCair said. "In neither of these instances did anyone go through the proper chain of command."

DeCair said senior department officials viewed the controversy over the three awards as obscuring the larger issue of superiors' right "to exercise managerial, policy and prosecutorial control" over the work of line attorneys. The controversy also diverted attention from employes who did receive major awards, including several agents and attorneys who distinguished themselves for undercover organized crime and drug investigations and other difficult prosecutions.