use strict; use warnings;
use List::Util qw(min);

my %seahash; my $date; my $time; my $coolflag; 

while(<DATA>){
 next if /^date\/time/;
 chomp;
 my ($date, $time, $lat, $lon, $depth, $flag, $coolflag, $otherflag) = split;
 # you could need the other variables later, so I save it
 # print $date, " ",$time, "  ", $coolflag,"\n"; # checkpoint
 push @{$seahash{$date . " " . $time}}, $coolflag;
}

while (my ($timestamp, $flags) = each (%seahash)) { 
            print $timestamp, " ", min(@{$flags}),"\n"}

__DATA__
date/time             lat, lon, depth, flag, flag, flag
21-sep-2012 01:00:00  0    0    -200    a    1     c
21-sep-2012 01:00:00  0    0    -100    a    9     c
20-sep-2012 02:20:00  0    0   -1500    a    2     c
20-sep-2012 02:20:00  0    0    -500    a    4     c
20-sep-2012 02:20:00  0    0    -400    a    3     c
20-sep-2012 02:20:00  0    0    -300    a    3     c
10-Aug-2012 02:20:00  0    0    -200    a    3     c
10-Aug-2012 02:20:00  0    0    -200    a    1     c
10-Aug-2012 02:20:00  0    0    -200    a    7     c