#!/usr/bin/perl

use warnings;
use strict;

my @a = ("12;;654;Test;12345;Test", "13;;265;Test;12345;Test");

foreach my $line (@a) {
    chomp($line);
    my @b = split(";", $line);
    foreach my $i (@b) {
        if ($i eq "") {
            # Assigning a value to $i here changes @b too:
            $i = "000000";
        }
        # isdigit?:
        if ($i !~ /\D/) {
            $i = sprintf("%06d", $i);
        }
    }
    print join(";", @b) . "\n";
}