Tourists sitting on the bus' open-air top deck were hurt when they were hit by branches from the tree on Valletta Road, sources told Times of Malta.
Two of those struck - a Belgian man, 62 and a Spanish woman, 37 - died on the spot, with six others critically hurt, Health Minister Chris Fearne confirmed.
The police said three of the six critically injured were Britons - two boys aged six and eight and a man aged 44. The others were a German woman, 31, an Italian woman, 72, and a 35-year-old man whose nationality is not yet known.
It is not known whether the tree branches the bus hit had been damaged by Sunday night's gale-force winds.
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