A federal grand jury in Manhattan indicted three reputed organizedcrime figures yesterday, accusing them of controlling sections of the New York waterfront and top local officials of the corruption-plagued longshoremen's union.

The 245-count racketeering and extortion indictment is the latest in a continuing, three-year-old FBI investigation that has decimated the leadership ranks of the International Longshoremen's Association from New York to Miami.

Michael Clemente, a 71-year-old former ILA official from Brooklyn, was charged with tawking more than $1 million from officials of a Brazilian shipping company from 1973 through 1978.

Though it was not mentioned in the indictment, Clemente has been indetified by law enforcement officials as a member of the Genovese organizedcrime family. He is alleged to control the Manhattan waterfront.

Tino Fiumara, 38, of Wyckoff, N.J., another reputed member of the Genovese family, was charged with racketeering and extortion in controlling New Jersey ports and the activities of three ILA local presicents who were also indicted. Michael Copolla, a Fiumara "associate," was charged, too.

Six weeks ago, Anthony M. Scotto, ILA vice president with state and national political connections, was indicted in New York on similar charges. He has been identified as a member of the Gambino organizedcrime family who allegedly controls the Brooklyn and Staten Island docks.

Scotto, who has organized campaign frllies for President Carter and New York Gov. Hugh Carey, has denied the accusations, calling them the result of a Justice Department vendetta.

Prosecutors have turned over to Scotto's attorneys 1,100 hours of tapes from electronic "bugs" planted in his office and the office of a shipping official now reportedly a government witness.

Several other ILA officials and shipping company executives are now on trial in Miami on similar charges of extorting or paying huge sums for labor peace.

ILA officials at the union's New York headquarters could not be reached for comment yesterday on the latest indictments.

The grand jury charges are reminiscent of the award-winning Marlon Brando movie, "On the Waterfront." A racketeering count alleges, for in stance, that Clemente and Fiumara divided up parts of the port of New York.

Members of the criminal enterprise "recognized each other's control and influence within their respective territories and recognized and respected each other's membership in the enterprise because of each individual's position of respect, control and influence over a segment of business and other georgraphic areas..;" the indictment said.

A conspiracy count charges that the defendants continued their corrupt operation despite warnings that federal investigators were nearby.

For instance, on May 19, 1978, indicted ILA official Thomas Buzzanca allegedly took a $2,000 cash payment from a shipping company official who told him in a restaurant men's room that the FBI was "all over."

"Business as usual," Buzzanca, president of a New York City ILA local, was said to have replied.

Vincent Colucci, president of two Newark ILA locals, and Carol Gardner, president of another Newark ILA local, also were indicted, as were five shipping company executives.

While the 54-page indictment goes into great detail on transactions as small as $50, it devotes only one paragraph to Clemente's alleged acceptance of $1 million over the years from Netumar International, Inc., of New York City. Netumar is agent for a Brazilian shipping company that used Pier 36 on Manhattan's Lower East Side.

Robert B. Fiske Jr., U.S. attorney for the Southern District of New York, refused to elaborate on government evidence about the alleged $1 million payoff, or what "economic benefits" the shipper got for his money.

Fiske said in a phone interview that the ongoing inquiry "is a model investigation from my point of view. The FBI has taken a lot of hard knocks in recent years. The agents who have worked on this case ought to get a lot of credit for this."

Soruces familiar with the ivestigation said Clemente was imprisoned in the 1660s on income tax charges and that Fiumara and Copolla, the other two reputed organized-crime figures charged, are now under indictment in New Jersey on other federal charges.