The Catholic bishop of Ponce was standing before a makeshift wooden altar and looking out at the 200 Haitian refugees seated on rows of newly built benches.

"Perhaps you have heard voices saying that you are not wanted here, but those persons do not represent the people of Puerto Rico," Bishop Juan Fremiot Torres said. "I pray . . . that at the end of these legal proceedings, the outcome is that you may stay in American territory, of which Puerto Rico is a part."

The bishop's message, delivered last Sunday at the U.S. government's new refugee detention center here, was translated into Creole while Puerto Rican Gov. Carlos Romero-Barcelo and Cabinet aides, who had stopped by to check the facilities, listened.

It was not the message the refugees, most of them men in their 20s and 30s, had been expected to hear when they started arriving in Puerto Rico a week ago. Certain political leaders identified with Romero's statehood-for-Puerto Rico stand had been urging a protest. But the protest didn't catch fire. Sympathy for the Haitians doused it.

Fort Allen is located on an isolated, scorchingly hot plain near Puerto Rico's south coast, about 70 miles from the capital city of San Juan. There are permanent quarters at Fort Allen, air-conditioned and currently unused, but the government built a 10-acre tent city to house the refugees.

Photos of the tent city, the long strands of barbed wire that surround it, the squads of armed guards patrolling the compound, conjured up visions of concentration camps -- distressing visions to many Puerto Ricans. Many of this island's residents had been "boat people" in their day, and they found no concentration camps when they migrated.

Immigration authorities contend the empty quarters at Fort Allen will be occupied, at least partly, by staffers as the refugees continue arriving.

Romero initially had balked at accepting Haitians when they were to be sent here last year, an election year. Recently, when new efforts to block their transfer failed, Romero extracted promises from the Reagan administration that no more than 800 Haitians would be deposited here at any one time, and that the Haitians would not be permitted to settle in Puerto Rico if they are not deported back to Haiti.

But that was before public opinion warmed to the Haitians. Now Romero zestfully pummels his political opposition, saying that the cheers for the Haitian refugees "shut the mouth of those who underrated the charitable spirit of the Puerto Rican people."

His secretary of justice, Hector Reichard, has pledged to make sure that the refugees get adequate legal counsel when deportation hearings begin later this month. And Romero now promises that if he gets "clear signals" from the public he will reconsider his opposition to having Haitians resettle here.

Some of the clearest signals will likely come from island planters, who long have complained they cannot find farm workers despite the island's 20 percent unemployment rate. Haitians, regarded as the Caribbean's most industrious people, supposedly will resolve the planters' dilemma.