Six men were arrested yesterday and charged with participating in a major cocaine trafficking operation that used secret hiding places in cars to transport more than 165 pounds of the drug from Miami to the Washington area for distribution, according to the FBI.

The men, three of whom were arrested in Miami, were charged in a 71-page, 38-count indictment in U.S. District Court in Alexandria that was handed up May 13 and unsealed yesterday.

An FBI spokesman said the indictments and arrests capped a two-year investigation of a major cocaine trafficking organization based in Miami and responsible for transporting more than $2 million of the drug to the Washington area since November 1983.

Charged in the indictment with conspiracy to possess with intent to distribute and to distribute cocaine were Ruben Almaguer, 54, Nilo Alberto Nunez, 26, and Julio Antonio Paredes, 27, all of Miami; Warren Rudolph Cooper, 56, of Washington; Philip Lance Gelfo, 53, of Cheverly, and James Michael Sita, 48, of Upper Marlboro.

Two men charged in the indictment -- Jose Humberto Otero and Jorge Luis Suarez, whose addresses were not available -- remain at large, according to a spokesman for the U.S. attorney's office in Alexandria.

Almaguer, Nunez and Otero were also charged with continuing criminal enterprise, which an FBI spokesman said indicates that they were the leaders of the alleged organization. He said the charge is brought against persons suspected of supervising five or more other persons.

Gelfo and Sita also were charged in the indictment with making false declarations before a grand jury and obstruction of justice for allegedly lying before the grand jury when they testified about their involvement with other members of the alleged organization.

The FBI spokesman said the cocaine was brought to the D.C. area almost exclusively by car, hidden in bumpers and door panels and behind seats.

According to the indictment, as much as 50 kilograms of cocaine was sent to this area in a single shipment and as much as $185,000 in cash was passed at various meetings in local restaurants and in two Alexandria apartments used to store the drugs.