By GENE MILLER

Radio Havana asserted Saturday that a machine gun attack on two fishing boats from Cuba was inspired "by threats against Cuba by the highest authorities in the United States government."

A letter of protest has been sent to the United States through the Czechoslovakian embassy, Radio Havana reported.

The attack, which left one man dead and apparently three others injured from another vessel, "had all the characteristics of similar actions perpetrated before from the territory of the United States by counter-revolutionary bands determined to take revenge on simple working Cubans," the letter charged.

IN WASHINGTON, a State Department spokesman acknowledged receiving the letter. "We are studying it," he said.

The letter claimed that similar attacks in the past have been "inspired, organized and protected by the Central Intelligence Agency."

The latest attack, the letter declared, comes "in an atmosphere recently created through attacks and threats against Cuba by the highest authorities in the United States government."

The comment apparently referred to recent statements by U.S. officials about overseas military actions by Cuba; specifically, the presence of Cuban troops in Angola.

On March 15 the Joint Chiefs of Staff at the Pentagon said it was "reviewing contingency plans or possibly military action that might be taken against Cuba."

ON MARCH 26 Secretary of State Henry A. Kissinger said U.S. contingency plans are aimed at trying to caution the Soviet Union and Cuba that further intervention in Africa could have serious consequence.

Radio Havana, as monitored in Miami, described the attacking vessel as a "North American ship of the tugboat type, painted in white."

Said the Havana announcer: "The newspaper Granma reports today that a pirate launch manned by men without a country cowardly attacked two Cuban fishing boats, sinking them, murdering one crewman and wounding others, when the vessels were in international waters between Cuba and the United States."

By telephone to a Miami Spanish-speaking station at noon Thursday, a man who didn't identify himself claimed responsibility for the attack by the Cuban National Liberation Front and Brigade 2506.

Juan Perez Franco president of I Brigade 2506, the exile association of veterans of the Bay of Pigs, later said he had "no official knowledge of the attack."

But, he added, "We congratulate them for carrying out operations of this type. Those are spy ships, and their attackers represent a free Cuba."

A representative from the Czech embassy in Washington, meanwhile, arrived in Miami to arrange for the four Cuban seamen to return home.

The first boat to be attacked with the "Ferro 123," Radio Havana said. "It sank after being hit with sustained bursts of machine gun fire and the crew, three of them wounded, got into a life raft and drifted for two days before beaching on Cay Sal off Cuba's northern coast.

THE ATTACK vessel then shot up the "Ferro 119," killing one man and sinking the boat, the broadcast said.

The second attack was widely reported in the U.S. after a Norwegian cargo ship picked up four survivors and a dead man before dawn Thursday and brought them to Miami.

The dead man, Bienvenido Amauri Diaz, about 20, had been hit in the arm by a heavy caliber projectile and bled to death.

The FBI in Miami entered the case immediately, trying to establish if Cuban exiles in South Florida had violated the Neutrality Act.

The FBI said the fishermen were unarmed and defenseless. "They didn't even have a rifle to shoot sharks," an agent said.

The Havana Radio broadcast challenged American authorities to arrest and prosecute those responsible for the incident.

"ACCORDING TO wire reports from the United States, these mercenary bands have publicly attributed to themselves the responsibility of the repugnant crime," Radio Havana said.