Try this. I have replaced your hash with numeric keys with a simple 2D array. You will need to activate the lines marked ##, comment out or remove those marked #test, print to the file your want and build your @files array using readdir.

#!perl
use strict;
use warnings;
my @test = (470,278); #test

my @Gkel=();
my @Gkel_gz=();
my @TT1=();
my @files = qw(
  Gkel_check.1.ABC.dat.gz
  Gkel_check.1.ABC.dat
  check.1.ABC_TT1.dat
  check.1.AB_TT1.dat
);

foreach my $file (@files) {    
  if ( $file =~ m/^Gkel_/ ){
    if ( substr($file, -2) eq 'gz' ) {
     
      ## my $result = `gunzip -c $file|tail -1`;
      ## system(`gunzip -f $file`);
      
      ## my $count = substr($result,22,8);
      my $count = 108418; #test
  
      $Gkel_gz[0] = $file;
      $Gkel_gz[1] = $count;
    } else {
      
      ## my $result = `wc -l $file`;
      ## my ($count, $file_name) = split(' ',$result);
      my $file1 = substr($file,5);  
      my $count = 107948; #test
      ## system(`mv $file $file1`);

      $Gkel[0] = $file1;
      $Gkel[1] = $count;
    }
  } 
  
  if ( $file =~ m/^check.*TT1.dat$/ ){
    ## my $result = `wc -l $file`;
    ## my ($count, $file_name) = split(' ',$result);
    my $count = shift @test; #test
    push @TT1,[$file,$count];
  }
    
}

# Expected
#Gkel_check.1.ABC.dat.gz    108,418    108,418    
#check.1.ABC_TT1.dat    470    
#check.1.ABC.dat 107,670    107,670 TRUE
#check.1.AB_TT1.dat    278       

my $Count  = $Gkel_gz[1];
my $Count1 = $Gkel[1] - $TT1[1]->[1] ;

my @row = ('Jun-2013',
$Gkel_gz[0],$Count,$Count,
$TT1[0]->[0],$TT1[0]->[1],
$Gkel[0],$Count1,$Count1,
'TRUE',
$TT1[1]->[0],$TT1[1]->[1]);
print join ',',@row,"\n"
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