BY JAY WEAVER

A Florida International University professor and his wife, an FIU counselor, pleaded not guilty today at an arraignment hearing in Miami federal court.

The couple are accused of operating as covert agents for Cuba's communist government for decades, using shortwave radios, numerical-code language and computer-encrypted files to send information about Miami's exile community to top Castro intelligence commanders.

Carlos M. Alvarez, 61, and his wife, Elsa, 55, were denied bond on Jan. 9 by U.S. Magistrate Judge Andrea Simonton. The couple are facing a charge of failing to register with the federal government as foreign agents.

Simonton said she believed that the gravity of the charges -- allegedly admitted by the couple last summer to the FBI -- their past academic trips to Cuba and their contacts in Fidel Castro's government made them a flight risk if allowed to return to their South Miami home.

Their attorneys, Steven Chaykin and Jane Moscowitz, plan to appeal Simonton's decision, which has kept the couple in detention in solitary confinement in the Federal Detention Center in downtown Miami.

''We think they are being inappropriately detained,'' Chaykin said after the brief arraignment attended by two of the couple's four sons. ``Their presumption of innocence has been eviscerated. They are being punished for a crime they were not convicted of.''

Moscowitz said it has been particularly hard for her client, Elsa, to be separated from the couple's 12-year-old daughter.

''She is in distress,'' Moscowitz said. ``But somedays she is full of fire. She is ready to fight.''

The indictment, which included no mention of top-secret U.S. government information being disclosed, came months after the couple's admission because of additional investigative work in the case, interim U.S. Attorney R. Alexander Acosta said.

Their confessions were videotaped this summer, according to one law enforcement source familiar with the case.

But the couple's attorneys dispute that claim. They said that some of Carlos Alvarez's statements may have been videotaped by the FBI, but that Elsa Alvarez's statements were not recorded in any way.

The case of the longtime FIU employees marks the biggest Miami spy-related case since 1998, when five men were charged with infiltrating the exile community and laying the groundwork for the shootdown of four Brothers to the Rescue pilots by the Cuban Air Force in 1996.