MIAMI - Premier Fidel Castro said two "pirate gunboats" attacked the Havana waterfront at dawn today and he charged that the United States Government was responsible.

Angrily, he attributed the assault directly to United States-based exiles, "those villains at the service of imperialism and reaction."

Earlier, the Havana radio, in a short communique, said that only one "pirate gunboat strafed Havana's waterfront with 50-mm. machine-gun shells that hit several buildings near Maceo Park in the central part of the city.

In a speech delivered this morning from the top of Cuba's highest mountain, Mount Turquino, in Oriente Province, and monitored here, the Premier said that about 2:45 A.M. one gunboat opened fire.

He added that three or four minutes later, "apparently trying to hit the house of the President," Dr. Osvaldo Dorticos Torrado, a second boat sprayed bullets over the Miramar residential district, about five miles west of the first objective, hitting the national aquarium.

Neither the communique nor Premier Castro reported any casualties.

"Whom are we to hold responsible for this [attack] but the United States Government and the C.I.A., which have perpetrated all types of crimes against our country," Premier Castro said.

Although accusing the United States, the Premier added that these attacks were "not bad but good" for the revolution because "we shall know how to behave as what we are: Their irreconcilable enemies."

He went on: "Because, in reality, we do not want any peace with Imperialism as long as it exists. And as long as there are victims of imperialist aggression and as long as in awry part of the world there are peoples fighting against imperialism, their cause will be our cause."

Mr. Castro did not indicate whether the strafing of Havana would affect the United States-Cuban agreement to let 3,000 to 4,000 Cubans leave the island monthly.

108 Exiles Arrive

Yesterday the first United States-chartered boat brought to Key West 108 exiles of the reported 2,000 Cubans stranded in the point of Camarioca when the Castro regime suspended the small-boat exodus. A regular Matanzas-Miami air shuttle is expected to begin around Dec. 1.

In Miami, an anti-Castro group, called Cuban Representation in Exile, said its boats had been responsible for today's attack on Havana. The group said the vessels had "returned safely to their bases somewhere in the Caribbean."

This was the second strafing of the Cuban capital by exiles. An anti-Castro student group in Miami said it staged the earlier one in August, 1962.

Premier Castro's 50-minute speech, one of his shortest, was delivered during a graduation ceremony for about 400 physicians and dentists. He said they had climbed Cuba's highest mountain to prove "their revolutionary fervor."

The ascent, he said, was a "symbol of the revolutionary spirit" He said the mountain inspired "new faith in the virtues of the revolution."