Conille, escorted by Haitian police and members of a UN-backed Kenyan security force, was able to flee the area unharmed.
Video footage showed several police officers running to take cover as shots rang out. It has not been announced if there were any injuries.
The hospital building was under gang control from the end of February until early July, when a police operation succeeded in taking it back.
Criminal groups control some 80 percent of Port-au-Prince, with residents saying they have faced the threat of murder, rape and kidnapping for ransom.Hundreds of police officers from Kenya have been deployed in Haiti’s capital, part of an international effort to bring stability to a country riven by political, social and economic chaos.Conille has vowed to restore the authority of the state. He came to office as part of an interim government that was formed following the resignation of his unpopular and unelected predecessor, Ariel Henry.