England captain Raoni Medina put his team ahead after two minutes but the Maltese side equalised through Andy Mangion on six minutes.
The score remained one-all for the next six minutes but England gained the upperhand when Luke Ballinger gave them a 2-1 lead. They added two more goals, through Medina (16) and Maximilian Kilman (19), for a 4-1 half-time lead.
William Wallace (22) and Kilman (34) were on target in the second half as England emerged 6-1 winners.
Malta, led by coach Peter Pullicino, meet hosts Bulgaria in their second game on Wednesday while, on the same day, England take on Albania.
The Maltese side end their group commitments on Friday with a match against Albania.