The warning that you comment is due to:

$delay_ATO_CTO_min = "";
[download]

After that assignment you try to use $delay_ATO_CTO_min as a number:

if ($delay_ATO_CTO_min > 10){
[download]

Nevertheless, the script you posted doesn't seem to parse the input file you provided (the fields in the input file are not separated by ";", you don't check for "empty" lines (e.g. lines with only the time), etc...). Here is a version of your script with some of these problems corrected:

use strict;
use warnings;

while (<DATA>){

  chomp($_);
  my ($aircraft_id,$ATO,$ATO_min,$CTO,$CTO_min) = (split /\s+/)[1,2,3,
+4,5];

  next if (!defined $ATO);

  my $delay_ATO_CTO_min = 0;

  if ((defined $CTO  && $CTO =~ /\d\d:\d\d/) && (defined $ATO && $ATO 
+=~/\d\d:\d\d/)){
    $delay_ATO_CTO_min = $CTO_min-$ATO_min;
  }

  my $flight_big_delay;
  # condition on the delay
  if ($delay_ATO_CTO_min > 10){
    $flight_big_delay = $aircraft_id;
    print "$aircraft_id;$ATO_min;$CTO_min;$delay_ATO_CTO_min;$flight_b
+ig_delay\n";
  }
  else{
    print "$aircraft_id;$ATO_min;$CTO_min;$delay_ATO_CTO_min\n";
  }
}

__DATA__
08:48:45
08:49:43    DAL11    08:47    527    08:50    530
08:50:41
08:51:40
08:52:38
08:53:36    ACA87    08:51    531    08:53    533
08:54:35
08:55:33    SHT8K    08:48    528    08:55    535
08:56:31
08:57:30    DLH9F    08:53    533    08:57    537
[download]

Outputs:

DAL11;527;530;3
ACA87;531;533;2
SHT8K;528;535;7
DLH9F;533;537;4
[download]

citromatik