A federal judge yesterday issued a temporary restraining order blocking a decision by the Carter administration to send Cuban and Haitian refugees to Puerto Rico.

Judge Juan R. Torruella acted on a motion submitted to him last week by the government of Puerto Rico, which filed suit against the administration plan.

Justice Department attorneys said they will take the decision to the U.S. Court of Appeals in Boston.

When it was first announced that Cuban and Haitian refugees would be sent to this Caribbean U.S. commonwealth, authorities estimated that as many as 19,000 would be processed here. The figure later was reduced to 5,000 and again to about 2,000. The first group had been scheduled to arrive about Oct. 15.

Between 15,000 and 25,000 Haitians have fled their homes over the past few years, primarily to the United States. An estimated 125,000 Cubans fled to the United States beginning in mid-April and many have been housed since then in temporary holding facilities across the country.

Yesterday, at one of those facilities, Fort Chaffee, Ark., dozens of Cuban refugees brandishing chairs charged an officer searching for stolen goods in a building reserved for troublemakers. Five detention officers and three refugees were injured.