The Carter administration is preparing two more military bases, the former Bainbridge Naval Training Station, Md., and Indiantown Gap, Pa., to handle the continuing flow of Cuban exiles leaving south Florida, according to the White House.

A White House spokesman said last night that presidential assistant Jack Watson has asked the Defense Department to prepare the two bases -- the first in the East -- to be ready, if needed, to accept arrivals in the next few weeks.

Indiantown Gap, a National Guard training center in southeastern Pennsylvania that housed Vietnamese refugees in the mid-1970s, is expected to be ready in a week to 10 days, with Bainbridge, which is about 35 miles northeast of Baltimore, ready about a week later, he said. Each is likely to hold 20,000 people if the refugee flow continues at its current rate.

Another 5,000 exiles arrived in Key West yesterday to bring the total to about 35,000 over the last three weeks. Federal officials calculate that Fort Chaffee, Ark., will be filled to its 20,000 capacity by next Sunday. Eglin Air Force Base in the Florida panhandle is also processing thousands of the new arrivals.

John Macy, director of the Federal Emergency Management Agency, which is coordinating the processing, said last night that "we're looking at quite a number of sites because of the high arrival rate and the low resettlement rate. We want to be prepared."

The readying of multiple processing centers is reminiscent of the response to the emergency migration of 150,000 Vietnamese in 1975 and 170,000 more Indochinese since late 1978. Both Chaffee and Indiantown Gap were used to handle Southeast Asian refugees before they were resettled.

Carter administration officials have been frustrated handling the flow of exiles because Cuban President Fidel Castro is dictating the rate at which they leave his island for the boat trip across the Florida Straits. The latest administration strategy is to bring international pressure on Castro to force him to allow an orderly Havana porcessing -- and thus a controlled flow -- of the refugees.

Federal policy toward the new "boat people" has been complicated by conflicting goals -- a desire to accept people fleeing Castro's communist regime, and an effort to stem the flow of refugees that threatens to strain the nation's budget as the economy worsens, with a potential backlash.

Meanwhile, the boats continue to arrive. Those refugees with relatives in the Miami area, the center of the Cuban community that fled Castro in the 1960s, are being sent there after initial processing in Key West.

Phil Zaferopulos, a federal official in Miami, said last night that more than 15,000 Cubans have already been processed through Miami, and another 3,000 or so are still at Opa Locka airport north of Miami awaiting release to relatives.

Those refugees without relatives in the United States are the ones now being sent to the Eglin and Chaffee centers, and the same procedure is envisioned for Bainbridge and Indiantown Gap.

At Fort Chaffee yesterday, refugees streamed in by the planeload. Base officials said the refugee count should be 4,300 by midnight, with about 3,000 coming each day for the remainder of the week.

Officials said 15,000 refugees would be housed at Chaffee -- a sprawling 73,000-acre complex near Fort Smith -- by Thursday and the 20,000 capacity mark would be reached by Sunday.

"Every time you look up, another plane's landing," a Chaffee spokesman said.

Lt. Col. Chris Crescioni said "the quick arrivals have caused logistic problems, such as having enough buses and processing the refugees. It's a dynamic, growing situation."

As an afterthought, he added, "It's a mess."

The Cubans arriving at Fort Chaffee seemed tired and thin yet happy. Many had ragged clothes and their only possession was a Red Cross kit containing chewing gum, a razor, soap, a toothbrush and toothpaste.