Joanne Ou, a spokesperson for Taiwan's Ministry of Foreign Affairs, said the embassy was closed "for safety reasons" after the brazen murder of Moise on Wednesday.
"At dawn on the 8th (of July), embassy security discovered that a group of armed men had broken into the embassy courtyard. Security staff immediately notified embassy personnel and Haitian police," she told AFP.
"At the request of the Haitian government and to assist in apprehending the suspects, the embassy granted permission to the Haitian police to enter embassy grounds," she added.
In a statement posted on its website, Taiwan's embassy in Port-au-Prince described the men as "mercenaries" and suspects in Moise's assassination.
"The police launched an operation around 4pm (2000 GMT, Thursday) and successfully arrested 11 suspects. The process went smoothly," the statement said, describing Moise's assassination as "cruel and barbaric".
Haiti is one of just 15 nations that diplomatically recognises Taiwan over China. Most of them are small nations in Latin America and the Pacific.
Taipei's embassy in Port-au-Prince lies close to the hillside private residence where Moise was gunned down.