Robert Abela was met with jeers and chants of "shame on you" when he left his office at Auberge de Castille soon after a vigil for building collapse victim Jean Paul Sofia.
The prime minister, escorted by police officers and bodyguards, exited the building through the main door, where people were laying candles in front of a portrait of the young man who was last December crushed to death.
As he walked around the building to his car, he was met with shouts of "mafia" and "chicken".
Once he entered his car, someone threw a bottle at the vehicle.
A few hours before, he announced a public inquiry into Sofia’s death, after weeks of refusing to open a public investigation despite the relatives' heartfelt pleas and a PN motion.
In a press conference launching the inquiry, Abela attacked a magistrate for delaying her probe into the youth's death, and apologised for not showing solidarity with the youth's relatives.
At the vigil, Sofia's mother, Isabelle Bonnici thanked both the prime minister and the Opposition leader, whom she said ensured that a public inquiry took place.