Federal prosecutors filed tax charges yesterday against the former chief financial officer for Youth Pride Inc. in the first allegation of criminal violations brought so far as a result of the government's two-year-old investigation into the now-defunct self-help organization.

In papers filed in U.S. District Court, the government contended that Johnny Mickens III failed to file income tax returns and pay more than $16,000 in federal taxes for three years from 1977 through 1979. The charges, which are misdemeanors, each carry a penalty of one year in jail, a $10,000 fine or both.

Mickens, 35, who now lives in Hampton, Va., had worked for Youth Pride as its director of administration and had been an officer and director of one of its real estate spinoffs, P.I. Properties Inc. In those jobs, Mickens controlled the organization's finances and was a close associate of Youth Pride's executive director, Mary Treadwell.

The government's longstanding investigation has focused on allegations that Treadwell and two other officials of P.I. Properties, Robert E. Lee Jr. and Joan M. Booth, stole, diverted or misappropriated $600,000 from the federal government and low-income tenants at Clifton Terrace Apartments in Northwest Washington. Treadwell has denied any wrongdoing. Booth has refused to be interviewed, and Lee has declined to discuss specifics.

The government stated its charges against Mickens yesterday in a document known as a criminal "information." Customarily, when charges are filed in that form, instead of through a grand jury indictment, it indicates that the prosecution and the defense have already reached an agreement on a resolution of the case. Mickens is scheduled to appear Friday before Judge John Garrett Penn in connection with the charges.

Assistant U.S. Attorney William D. Pease, who has been supervising the Pride Investigation along with Assistant U.S. Attorney Stephen R. Spivack, refused to comment yesterday when asked if Mickens has been cooperating with the government or whether he has testified before a federal grand jury investigating the case.

Mickens could not be reached for comment late yesterday. His attorney, Barry Leibowitz, refused to comment on the allegations against his client.

The government alleged in court papers that Mickens had a total taxable income of $70,600 in 1977, 1978 and 1979 but did not file income tax returns or pay $16,124 in taxes owed to the government on those earnings.

Mickens worked for P.I. Properties from mid-1977 to late August of 1978, when the federal government took over control of Clifton Terrace apartments. Mickens had the authority to sign checks for the business and had oversight over financial matters and records.

The alleged offenses involving P.I. Properties took place between 1974 and 1978, and until recently those allegations had been considered the main focus of the investigation. Last November, however, federal prosecutors issued subpoenaes to 12 former and present City Council members, including Mayor Marion Barry, for all records on a now-abandoned plan to give a bus shelter contract to another Pride spinoff.

The request for records involved Pride Environmental Services Inc.

The council never formally voted on the bus stop proposal and a prime sponsor, council member Wilhelmina Rolark (D-Ward 8) withdrew her support saying she thought Treadwell was soliciting bids on a city franchise.

The prosecutors also asked for records on an exclusive 15-year trash can advertising contract that was awarded to PES in 1972 but canceled in 1980 for mismanagement. The council members turned records over to the prosecutors last month.