Angry Bangladeshi fans had stoned the Caribbean team's bus and home side skipper Shakib Al Hasan's home after the humiliating loss by nine wickets.
Hasina said such behaviour was "undesirable" and could adversely impact Bangladesh's chances of hosting international sporting events.
During a political rally here, Hasina said it was "not acceptable that you will garland the players if they win and pelt them with stones if they lose.".
Bangladesh were bowled out for 58 in the match which was their lowest one-day total.
The stoning incident after the game was earlier condemned by the ICC as well and led to an increase in security.
Bangladesh is co-hosting the World Cup along with India and Sri Lanka.
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