The U.S. Civil Service Commission - watchdog for the federal merit system - has hired a prominent, outside lawyer to investigate alleged abuses by the commission's own employees, including possible patronage malpractices dating from the Nixon era.

Mitchell Rogovin, a former assistant attorney general who recently represented the Central Intelligence Agency during congressional intelligence probes, was retained by CSC to conduct what was described as a "comprehensive and independent inquiry.

Rogovin and his aides will investigate recent allegations that senior CSC staff members have improperly obstructed some of the commission's own investigation into complaints of racial and sex discrimination.

In addition, Rogovin's investigative team has been asked by CSC to determine whether any CSC employees conspired with other government officials during the Nixon era to bypass the federal merit system in attempts to provide government jobs for the Nixon administration's political allies.

Rogovin said yesterday that he viewed his new investigation primrily as an administrative, rather than criminal, inquiry that could lead to possible disciplinary measures against CSC employees, including firing. He said he plans to take testimony from CSC employees under oath and added that if evidence of criminal wrongdoing is uncovered, it will be referred to the Justice Department for possible action.

A CSC spokesman said the commission hopes Rogovin's investigation will be completed in six months. Neither Rogovin nor the commission disclosed yesterday how much Rogovin's firm - Rogovin. Stern and Huge - would be paid for its investigative work.

The Civil Service Commission has been under congressional pressure to carry out an investigation of its own employee's alleged malpractices because of charges made by Clinton Smith, the commission's equal employment opportunity director.

In a Sept. 20 memorandum to CSC Chairman Alan K. Campbell. Smith alleged that senior CSC staff members had interfered with CSC investigations into discrimination complaints. He also charged that top CSC employees failed to take "corrective" action when alerted to merit system abuses, and he complained of "reprisal actions" taken against him be senior CSC employees, "including threats and attempts to divest him of major duties."

Smith's allegations were cited yesterday by CSC Chairman Campbell in his announcement of Rogovin's investigation.

Smith's allegations apparently are linked partly to a discrimination complaint lodged by Peggy Griffiths, a CSC lawyer, Griffiths, a black woman, had complained that she was a victim of discrimination at the hands of CSC officials. After she went to court, she won a $43,592-a-year job as chairman of the CSC appeals review board.

Smith, according to a CSC spokesman, had previously ruled in Griffiths' favor, finding that she was a victim of discrimination. According to an article in the Federal Times last month, Smith later charged in his memo that efforts by CSC employees to "intimidate" him acclerated after his Griffiths ruling.

In directing Rogovin to examine alleged patronage abuses dating from the Nixon era, the Civil Service Commission focused renewed attention on a series of charges that were the subject of administrative and congressional scrutiny several years ago.

The Civil Service Commission alleged in 1974 that employees of the General Services Administration and other agencies had previously circumvented the merit system in efforts to obtain government jobs for political favorites. Although 19 federal employees were eventually charged by CSC with patronage abuses, a CSC spokesman said yesterday, none of them was ever found guilty.

Since then, the spokesman added: suspicions have continued to be raised that some CSC employees may also have engaged in these alleged malpractices. "There are still questions: when are you going to punish those individuals who did wrong in that era?" the spokesman said. "These things have lingered to this day.

Rogovin's inquiry is apparently an attempt to put these suspicions finally to rest - either by recommending disciplinary or other local measures against some CSC employees or by concluding that no such action is warranted.

The Civil Service Commission has previously taken steps to curb its own alleged abuses. In 1975, the commission prohibited its members and employees from recommending applicants for federal jobs. This prohibition followed disclosure that on 35 occasions during the previous six years, three commission members had recommended job applicants to officials in federal agencies.