use Data::Dumper;

my %msg_rate = ('1', '00:00:00,284', '2', '00:00:00,462', '3', '01:01:00,462', '4', '00:02:00,462',
+'5', '01:03:00,462');

my %count_per_min;
while( my ($key1, $val1) = each(%msg_rate) ) {
    my ($hh1,$mm1,$ssms1) = split(/\:/,$val1);
    $count_per_min{"$hh1:$mm1"}++
}

print Dumper \%count_per_min;