You need to use the verbatim package, something such as this:

#!/usr/bin/perl

use strict;
use warnings;
use Tie::File;

__END__
-- test --
[% USE Latex;
      out = FILTER latex(format="pdf");
-%]
\usepackage{verbatim}
\begin{comment}
This is a comment
Ditto
Double-Ditto
\end{comment}
\documentationclass{article}
\begin{document}
\section{{Introduction}
\end{document}
[% END; -%]
[% out | head(4) %]
-- expect --
%PDF
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