A federal grand jury today indicted Geoffrey Lindenauer, former deputy director of New York's Parking Violations Bureau, on racketeering and extortion charges, declaring that he took more than $410,000 in bribes from city contractors.

The 39-count indictment against the protege of former Queens Borough president Donald R. Manes came after U.S. Attorney Rudolph W. Giuliani negotiated for weeks but failed to persuade Lindenauer to testify against Manes.

Lindenauer is to be arraigned Friday.

No charges have been filed against Manes, who slashed his wrist and ankle in a suicide attempt Jan. 10, four days before Lindenauer was charged on a single count of extorting $5,000 from a company that collected parking fines.

Since then, a second contractor has told federal prosecutors that he paid Lindenauer $36,000 in bribes after being ordered to do so by Manes, who resigned the borough presidency Feb. 11. Manes, as top official in a borough of 1.5 million people and chairman of its Democratic Party, was one of the city's most powerful politicians.

Giuliani told reporters today that the Lindenauer indictment "is the first case" in a widening corruption investigation. "It may not be the last case. We anticipate further charges."

Mayor Edward I. Koch told reporters today that, while he concentrated on the city's fiscal crisis over the last eight years, "my administration lost the distance and the controls I had hoped to maintain in order to avoid the undue influence of party leaders on the workings of government. We let our guard down, and now we're paying the price."

Koch has appointed former assistant U.S. attorney John Martin Jr. to investigate city contracts. In addition, corruption investigations are under way by the Brooklyn U.S. attorney, the state attorney general, the district attorneys of Manhattan, the Bronx, Brooklyn and Queens and by the city's Department of Investigations and Board of Ethics.

Lindenauer is a key figure in an investigation of the award of a $22.7 million contract for portable computers to a company partly owned by Bronx Democratic leader Stanley Friedman, a close Koch associate.

Koch said today that he and Gov. Mario M. Cuomo (D) will establish a joint commission to examine campaign-financing reforms and ways to "minimize the relationship between money, politics and government."