The judge said the Haitian journalist would probably be freed by tomorrow, though he did not explain the reasons, and would not say when Pina would be released.
Peres Paul said Pina struck him as officers tried to remove the reporter from the church. Pina denies striking the judge.
Pina has been reporting from Haiti for 10 years for ''Flashpoints," a daily program produced by radio station KPFA in Berkeley, Calif., and distributed to other stations by the Pacifica Radio Network, said Dennis Bernstein, the show's executive producer.
The two journalists and a few others went to the St. Claire church in Cazeau, a poor neighborhood of Port-au-Prince, after learning that police were searching the building.
Officials refused to disclose a reason for the operation, but police at the scene said they were looking for weapons.
Jean-Juste, a supporter of ousted President Jean-Bertrand Aristide, has been held since July on suspicion of involvement in the kidnapping and murder of a well-known journalist, Jacques Roche.
Jean-Juste, who has not been charged, denies the allegations. He has said he was in Miami when the crime was committed.
The Roman Catholic priest is considered a possible presidential candidate for Aristide's Lavalas Family party in Nov. 20 elections.
Aristide fled Haiti in February 2004 during an armed revolt and is exiled in South Africa.