For example:

use Time::Local;

while (<>) {
  my @line=split(";");
  my @start_time=($line[3]=~/(\d+)-(\d+)-(\d+)\s(\d+):(\d+):(\d+)/);  
+ #parsing the start time
  my @stop_time=($line[4]=~/(\d+)-(\d+)-(\d+)\s(\d+):(\d+):(\d+)/);  #
+parsing the stop time

  my $start_time = timelocal($start_time[5], $start_time[4], $start_ti
+me[3], $start_time[2], $start_time[1], $start_time[0]);

  my $end_time = timelocal($end_time[5], $end_time[4], $end_time[3], $
+end_time[2], $end_time[1], $end_time[0]);

  my $min_diff = sprintf("%.0f", ($end_time - $start_time) / 60);

  print $min_diff."\n";
}
[download]

(untested code)

Also, your rounding function is weird. Use (s)printf if you want correctly rounded numbers.