I have written the code and its working fine. Below is the code

print "Fetch in Progress - Tables\n";
my $sth = $dbh->prepare($sql1) or die $dbh->errstr;
$sth->execute() or die $dbh->errstr;

my $tlast ='';

open(INFILE1,">tempfile.txt");
open(INFILE2,">newtables.txt");
open(INFILE3,">updatetables.txt");

while (@data = $sth->fetchrow_array()) {

print INFILE1 (@data[0]."\t".@data[1]."\t".@data[2]."\t".@data[3]);
print INFILE1 ("\n");
}
close INFILE1;

open(INFILE1,"tempfile.txt");

my @contents=<INFILE1>;
close INFILE1;

open(INFILE1,"tempfile.txt");
while (<INFILE1>) {
    
    my @elements = split /\t/, $_;
    my $tc = @elements[0]."\t";
    
    if ($tc ne $tclast)    
    {  my @filtered = grep /$tc/, @contents;
       if ($#filtered ==0)
       { print INFILE2 (@filtered);}
       else
       {print INFILE3 (@filtered);}
    }
    $tclast=$tc;
}

close INFILE1;
close INFILE2;
close INFILE3;

print "Fetch in Progress - Column\n";

my $sth = $dbh->prepare($sql2) or die $dbh->errstr;
$sth->execute() or die $dbh->errstr;

my $tlast ='';

open(INFILE1,">tempfile1.txt");
open(INFILE2,">newcolumn.txt");
open(INFILE3,">updatecolumn.txt");

while (@data = $sth->fetchrow_array()) {
print INFILE1 (@data[0]."\t".@data[1]."\t".@data[2]."\t".@data[3]."\t"
+.@data[4]."\t".@data[5]."\t".@data[6]."\t".@data[7]."\t".@data[8]."\t
+".@data[9]."\t".@data[10]);
print INFILE1 ("\n");
}
close INFILE1;

open(INFILE1,"tempfile.txt");
my @contents=<INFILE1>;
close INFILE1;

open(INFILE1,"tempfile.txt");
while (<INFILE1>) {
    
    my @elements = split /\t/, $_;
    my $tc = @elements[1]."\t".@elements[2]."\t";
    
    if ($tc ne $tclast)    
    {  my @filtered = grep /$tc/, @contents;
       
       if ($#filtered ==0)
       { print INFILE2 (@filtered);}
       else
       {print INFILE3 (@filtered);}
    }

    $tclast=$tc;
}

close INFILE1;
close INFILE2;
close INFILE3;

print "Fetch in Progress - Indexes\n";

my $sth = $dbh->prepare($sql3) or die $dbh->errstr;
$sth->execute() or die $dbh->errstr;

my $tlast ='';
open(INFILE1,">tempfile.txt");
open(INFILE2,">newindexes.txt");
open(INFILE3,">updateindexes.txt");

while (@data = $sth->fetchrow_array()) {
print INFILE1 (@data[0]."\t".@data[1]."\t".@data[2]."\t".@data[3]."\t"
+.@data[4]);
print INFILE1 ("\n");
}
close INFILE1;

open(INFILE1,"tempfile.txt");

my @contents=<INFILE1>;
close INFILE1;

open(INFILE1,"tempfile.txt");
while (<INFILE1>) {
    
    my @elements = split /\t/, $_;
    my $tc = @elements[0]."\t".@elements[1]."\t";
    
    if ($tc ne $tclast)    
    {  my @filtered = grep /$tc/, @contents;
       if ($#filtered ==0)
       { print INFILE2 (@filtered);}
       else
       {print INFILE3 (@filtered);}
    }
    $tclast=$tc;
}

close INFILE1;
close INFILE2;
close INFILE3;

print "Database retrieval completed\n";
#
# Disconnect from database
#
$dbh->disconnect;

print "Summary Sheet in Progress\n";
my $SummarySheet='Perl.xls';
my $workbook = Spreadsheet::WriteExcel->new($SummarySheet);

$worksheet = $workbook->add_worksheet("New Tables");
$worksheet->set_column('A:C', 20); 

my $row_curr=1;
open(INFILE1,"newtables.txt");
while (<INFILE1>) {
    my @elements = split /\t/, $_;
    $worksheet->write($row_curr, 0,@elements[0]);
    $row_curr=$row_curr+1;
}
close INFILE1;

$worksheet = $workbook->add_worksheet("Modified Tables");
$worksheet->set_column('A:C', 20); 

my $row_curr=1;
my $cnt=1;
open(File3,"updatetables.txt");
while (<File3>) {
    my @elements = split /\t/, $_;
    
    if ($cnt%2==1)
        {$worksheet->write($row_curr, 0,"Rep1");}
    else
        {$worksheet->write($row_curr, 0,"Rep2");}
              
    $worksheet->write($row_curr, 1,@elements[0]);

    $cnt=$cnt+1;
    
    if ($cnt%2==1 and $cnt>1) 
    {$row_curr=$row_curr+1;}
    
    $row_curr=$row_curr+1;
    }
close INFILE1;

$worksheet = $workbook->add_worksheet("New Columns");
$worksheet->set_column('A:C', 20); 

my $row_curr=1;
open(INFILE1,"newcolumn.txt");
while (<INFILE1>) {
    my @elements = split /\t/, $_;
    $worksheet->write($row_curr, 0,@elements[1]);
    $worksheet->write($row_curr, 1,@elements[2]);
    $worksheet->write($row_curr, 2,@elements[3]);
    $row_curr=$row_curr+1;
    
}
close INFILE1;
$worksheet = $workbook->add_worksheet("Modified Columns");
$worksheet->set_column('A:C', 20); 

my $row_curr=1;
my $cnt=1;
open(INFILE1,"updatecolumn.txt");
while (<INFILE1>) {
    my @elements = split /\t/, $_;
    
    if ($cnt%2==1)
        {$worksheet->write($row_curr, 0,"Rep1");}
    else
        {$worksheet->write($row_curr, 0,"Rep2");}
                      
    $worksheet->write($row_curr, 1,@elements[1]);
    $worksheet->write($row_curr, 2,@elements[2]);
    $worksheet->write($row_curr, 3,@elements[3]);
    
    $cnt=$cnt+1;
    
    if ($cnt%2==1 and $cnt>1) 
    {$row_curr=$row_curr+1;}
    
    $row_curr=$row_curr+1;
    }
close INFILE1;
$worksheet = $workbook->add_worksheet("New Indexes");
$worksheet->set_column('A:C', 20); 

my $row_curr=1;
open(INFILE1,"newindexes.txt");
while (<INFILE1>) {
    my @elements = split /\t/, $_;
    $worksheet->write($row_curr, 0,@elements[0]);
    $worksheet->write($row_curr, 1,@elements[1]);
    $worksheet->write($row_curr, 2,@elements[2]);
    $worksheet->write($row_curr, 3,@elements[3]);
    $worksheet->write($row_curr, 4,@elements[4]);
    $row_curr=$row_curr+1;
    
}
close INFILE1;
$worksheet = $workbook->add_worksheet("Modified Indexes");
$worksheet->set_column('A:C', 20); 

my $row_curr=1;
my $cnt=1;
open(INFILE1,"updateindexes.txt");
while (<INFILE1>) {
    my @elements = split /\t/, $_;

    if ($cnt%2==1)
        {$worksheet->write($row_curr, 0,"Rep1");}
    else
        {$worksheet->write($row_curr, 0,"Rep2");}
              
                      
    $worksheet->write($row_curr, 1,@elements[0]);
    $worksheet->write($row_curr, 2,@elements[1]);
    $worksheet->write($row_curr, 3,@elements[2]);
    $worksheet->write($row_curr, 4,@elements[3]);
    $worksheet->write($row_curr, 5,@elements[4]);
    
    $cnt=$cnt+1;
    
    if ($cnt%2==1 and $cnt>1) 
    {$row_curr=$row_curr+1;}
    
    $row_curr=$row_curr+1;
    
}
print "Completed";
close INFILE1;
#remove temporaray files
unlink updatecolumn.txt;
unlink updateindexes.txt;
unlink updatetables.txt;
unlink newcolumn.txt;
unlink newindexes.txt;
unlink newtables.txt;
unlink tempfile.txt;

exit 0;
[download]

This is working fine. Though I am not an expert in perl but i have taken the help of all pointers given above and wrote this.

I wanted someone to review and check if it can improved. If there are lot of changes required then I would suggest to ignore this.

Also, there may be few code which is relavant to my requirement while copying data into excel (some formatting done, inserting blank row and etc). So you can ignore that part

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