Among the exhibits at the site are a reproduction of sleeping cells from the Auschwitz death camp, artifacts and documents that belonged to survivors who fled the Nazis to Porto.
The film shows how the community was shaken by the news that there were descendants of Jews in Portuguese villages who still practiced Jewish rituals mixed with Catholicism, known as Marranos.
The community has released an extensive and detailed report showing the evidence that the Portuguese government concocted a scandal where there was none.
As many as 4,000 Jews were brutally murdered in the Lisbon massacre between April 19 and 21, 1506.
Over the past decade, a community of roughly 1,000 Jews has materialized in Porto, thanks to a law that since 2015 has allowed the return of people whose ancestors were expelled.
Dig into the small city located just three hours outside of Lisbon: Where to wine and dine, what to see, and where to stay
The ceremony featured the lighting of a memorial flame in front of 500 students from schools across Portugal who took part in the event.
"I know you blame the Israelis, but this time someone from your side started it," said Rebelo de Sousa. "The Palestinian side started it. You can't blame Israel, you shouldn't have started it.
Portugal's Justice Minister argued that the country’s citizenship law for descendants of Sephardic Jews who were expelled during the Spanish Inquisition has served its purpose.
The graffiti was removed the same day and no arrest has been made.