In an apparent effort to defuse the politically sensitive Cuban-Haitian refugee problem in south Florida, the Carter administration announced yesterday that it will open another resettlement center for new arrivals -- in Puerto Rico.

The State Department's task force handling the resettlement said that Fort Allen, a Navy facility on the south coast of the island, is capable of taking more than 1,000 refugees by mid-October and can house 4,500 within two months.

Last night, however, a task force spokesman seemed to back off the initial announcement that the Puerto Rican facility could handle 4,500 persons. A lack of sewage facilities may limit Fort Allen's capacity to a "couple thousand" refugees, he said. "An evaluation of that will have to be made. The Army Corps of Engineers will have to look into that."

Though the announcement said the refugees would be processed for resettlement in the United States, critics immediately charged that the choice was politically motivated because Puerto Rico has no electoral votes. Critics also said it was cruel to ship the newcomers back past Cuba and Haiti to another island 1,000 miles from the mainland.

Since last spring, 122,000 cubans and 6,000 Haitians have arrived in the United States -- most in south Florida -- on small boats. About 200 a day continue to come ashore. The Florida congressional delegation has put pressure on the administration to move the makeshift processing camps from the Miami area, and officials promised last week that a new processing site would be found.

A task force spokesman said Fort Allen will be used to house new arrivals and "possibly some Cubans currently located at resettlement camps in the United States." But he emphasized that Cubans with mental disorders or serious felony offenses will not be sent to Fort Allen, as one press account suggested.

More than 10,000 Cubans, mostly single males, who are difficult to resettle, are still being held at centers in Wisconsin, Pennsylvania and Arkansas. They still will be consolidated at Fort Chaffee, Ark., by Oct. 15, the announcement said.

The refugees have been a political issue in these states, as well, because violent disturbances have broken out at some of the camps. Thus administration officials have acknowledged difficulty trying to find any community willing to take a new resettlement camp.

The refugees to be sent to Puerto Rico might include some of the Cubans and Haitians now being housed in much-criticized camps near Miami, a task force spokesman said.

Joaquin A. Marquez, director of the Puerto Rican office of federal administration in Washington said yesterday that he didn't feel Fort Allen was capable of holding the planned numbers of refugees.

"I don't want to charge the Carter administration with politics with this," he said. "But if the people of Puerto Rico had several congressmen and two senators things might have been different."

Marquez said that Puerto Rico "always has been hospitable to refugees. We're not shirking our responsibility. But we have real concerns about the adequacies of Fort Allen."

He estimated that it would take two months just to refurbish the base to take 800 Cubans and Haitians, at most.

In San Juan, Gov. Carlos Romero Barcelo told reporters that he accepted the plan on the condition that Puerto Rico get no more than 800 refugees at a time, far short of the numbers mentioned in the administration announcement.

Rick Schwartz, a Washington lawyer who sucessfully sued the federal government over the treatment of Haitians in south Florida, said yesterday that the Puerto Rico decision "clearly reflects a poltical judgment to keep the refugee problem in an area where there won't be political repercussions."

Schwartz said he feared that the government would be more likely to try to deport the Haitians from Puerto Rico than from the continental United States, and said he was examining the possibility of legal action to stop the move.

Sen. Bob Dole (R-Kan.), a member of the Senate Judiciary Committee, which heard administration officials testify on the refugee problem Friday, said yesterday that the decision was "heartless election-year politics" aimed at Florida's electoral votes.

Republican presidential candidate Ronald Reagan got an enthusiastic response from a Hispanic audience Monday night when he sharply criticized the administration's failures to deal with the refugee problem.

Art Brill, a spokesman for the Cuban-Haitian task forces referred questions about the politics of the decision to the White House. He said the Puerto Rican facility was one of the few available, and had the advantage of good climate and a Spanish-speaking population to help in processing.