The masked supporters hurled stones and struck the bus with sticks on its return to the team hotel in Genoa early on Sunday morning according to the Italian press, breaking the windscreen.
The supporters have issued death threats to the squad should they be relegated.
"No result, even a really bad one, can justify such behaviour," the club said in a statement.
Sampdoria have suffered a complete reversal in fortunes after finishing fourth last season, they are just a point above the relegation zone ahead of Sunday's matches.
Their two best players were allowed to leave in the January transfer window, ending the strike partnership of Antonio Cassano, who was forced out and joined AC Milan after making abusive remarks about the club president, and Giampaolo Pazzini, who was sold to Inter Milan.
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