U.S. Coast Guard helicopters airlifted 55 Cuban refugees "in extreme peril" to safety today after the 34-foot fishing vessel Prima Dona ran aground five miles south of Boca Chica Naval Air Station.

Cmdr. Samuel Dennis said the Coast Guard has answered more than a dozen search and rescue calls the last two days as the "Freedom Flotilla" continues to ferry refugees across the Florida Straits. More than 61,000 have arrived in the 29-day sealift, and officials believe that number could reach 100,000 or more by the end of the month.

"There are still roughly 1,000 boats over there," Dennis said of the flotilla of small boats anchored in Mariel harbor. "They have a potential for bringing another 30,000 to 50,000 people. We're basing that on 30 to 50 passengers per boat, but some boats are coming with 200 and 300 on them."

Dennis accused the Cuban government of "creating disaster" by sending boats overloaded with refugees into rough seas.

"It's approaching a criminal situation," he said. "We could have a horrible situation."

Fourteen refugees died Saturday when their 36-foot boat, overloaded with 52 passengers, capsized. The captain said Cuban authorities had forced him to take additional passengers and misled him about sea conditions.

A series of strongly worded messages to Cuban authorities has been brought to the attention of the 99 other nations that belong, along with Cuba and the United States, to the Safety of Life at Sea international treaty, according to a spokesman for Coast Guard Commandant Adm. John B. Hayes.

A State Department spokesman said Cuban officials have not responded to President Carter's proposal of last Wednesday that the U.S. government transport the refugees.

"Our efforts now are in less formal diplomatic channels, such as the Coast Guard, than trying to deal directly with the Cuban officials," the spokesman said.

About 70 refugee-laden boats waited off docks here today as federal officials tried to keep the flow of new arrivals moving to centers in Miami, Fort Chaffee, Ark., and Fort Indiantown Gap, Pa.

At Fort Chaffee, authorities said that refugee processing center would reach capacity by tonight, with 20,000 Cubans undergoing health examinations and interviews. The Indiantown Gap facility, which opened Sunday, is to take the overflow from Chaffee.

Should that facility also prove inadequate, the government has announced it will use Camp McCoy, Wis., an Army training installation, as a temporary housing site for the refugees. Camp McCoy could be ready to house up to 15,000 refugees within 10 days, the Defense Department said.

Meanwhile, the Coast Guard barrier patrols operating along the Florida Keys from Dry Tortugas to Miami appeared to be stopping the flow of boats southward to Cuba. Dennis said three boats were turned back Sunday night.