CHICAGO (AP) _ An Italian agriculture conglomerate and its U.S. subsidiary agreed to pay the Chicago Board of Trade $2 million to settle claims that the company tried to manipulate the soybean futures market, both sides said Friday.

Ferruzzi Finanziaria S.p.A. will pay $1.65 million and its Central Soya Co. subsidiary will pay $350,000. They both will pay other expenses associated with the protracted legal battle.

Mark Prout, a BOT spokesman, called it a fine and said it was the largest in board history. But Ferruzzi spokesman Larry Friedman said the payments are not a fine because there wasn't any admission of wrongdoing.

''The settlement vindicates the group and clears it of allegations that it was in any way trying to influence the market,'' said David Swanson, a member of the Ferruzzi Group's strategic committee and president and chief executive officer of Central Soya.

Ferruzzi also agreed to resign its board membership and transfer its seat to Soya. The company also dropped its lawsuit against the BOT.

''We think this case is buried now for good,'' said Larry Friedman, a Ferruzzi spokesman.

BOT president and chief operating officer Thomas R. Donovan said the settlement ''puts the matter to rest.''

On July 11, 1989, the board issued an order requiring traders to reduce their holdings in contracts for July delivery of soybeans. The result was a steep drop in soybean prices on the cash and futures markets.

The BOT, the world's largest soybean futures market, issued the order to force the Italian grain company to reduce soybean holdings the exchange said threatened to cause a sharp, artificial increase in prices. Ferruzzi at the time held contracts to buy 23 million bushels of soybeans and owned more than half of the 12 million bushels available for delivery.