MSF says that on 11 November one of its ambulances carrying three young men with gunshot wounds was stopped by Haitian law enforcement officers.
Apparently supported by a paramilitary self-defence group, the men attacked the vehicle, removed two of the patients, took them outside hospital grounds and executed them.
The humanitarian group denounced the violence in a strongly worded statement last week, saying their personnel had been tear-gassed and held against their will for several hours.
While that incident appears to have been the final straw for MSF in Port-au-Prince, at least for the time being, it was not the only recent example of extreme aggression against their staff.
The announcement comes amid a worsening climate of violence in Haiti with some 25 suspected gang members killed in the capital on Tuesday.
The police say that residents helped officers to fight off an attempted attack on the upscale suburb of Pétion-Ville.
The neighbourhood was cordoned off after residents barricaded streets, some armed with machetes and makeshift weapons, in an apparent effort to prevent a gang invasion.