Federal prosecutors yesterday charged a niece of Senate Minority Leader Robert C. Byrd (D-W.Va.) with embezzling more than $12,000 from the Senate Post Office while she worked there as chief clerk.

The government charged in papers filed in U.S. District Court here that Barbara Ann Bowman, 44, periodically took money from the post office cash bank, which she used for her personal expenses, and at one time put back $2,000 in order to conceal the embezzlement from General Accounting Office auditors. Bowman lives at 3340 Willow Crescent Dr., Fairfax.

Bowman was charged yesterday with one count of theft of government money and one count of covering up the loss of funds in order to mislead the GAO investigators. As the chief clerk, Bowman, who earned $24,000 a year, had control over two drawers of cash totaling $20,000, according to court records.

Law enforcement sources said that Bowman allegedly used some of the funds to pay rent and to make payments on a credit union loan. According to court papers, Bowman allegedly took the money between Sept. 2, 1980, when she began work at the post office, and Aug. 17, when she was placed on administrative leave. She later resigned.

Senate Sergeant-at-Arms Howard S. Liebengood, whose office operates the Senate Post office, said yesterday that he was informed on Aug. 10 that a "significant amount of funds" was unaccounted for after an unscheduled GAO audit. The Capitol Police began an investigation into the case on Aug. 11, Liebengood said.

On Aug. 12, however, Liebengood said he suspended the police investigation pending an "internal investigation" by his office after Bowman called him and asked for a meeting and then agreed to tell what she knew about the loss of funds from the post office. An aide to Byrd and Majority Leader Howard H. Baker Jr. (R-Tenn.) were both informed of the investigation, Liebengood said.

Law enforcement officials expressed concern yesterday that Liebengood's decision to have his office investigate the case, instead of the police, could have jeopardized the rights of suspects who could later be involved in criminal prosecutions.

Liebengood, whose office also oversees the Capitol Police, said he asked the police to hold up any further investigation because he believed that an elaborate police effort would not be necessary since Bowman has allegedly agreed to cooperate with Liebengood's office. Liebengood said Bowman was allowed to remain on the job because she was cooperating with officials but that she then had no access to the safe where money was held at the post office.

Five days later, however, Bowman was placed on administrative leave after another, unannounced GAO audit uncovered further discrepancies in accounts at the Senate Post Office, according to Liebengood's deputy, Larry Smith. Smith had been conducting an internal investigation into the post office case while Liebengood was on a two-week trip to China.

Liebengood said he returned to his office on Aug. 31, read Smith's report on the case, accepted Bowman's resignation and told the Capitol Police to take the case to the U.S. attorney's office. Liebengood said he called Baker in Tennessee that day to inform him of the results of the case.

As a result of the investigations into losses at the Senate, another employe there was dismissed, one was transferred to other duties and four letters of reprimand were issued, Liebengood said.