$s = '1 <% xxx%%> 2 <%%> 3 <%>%> 4 <% >% %> 5 <%%%% xxx %%%%> 6 ';

$s =~ s/<% (?> [^%]+ | %+ [^>]+ )* %>/!REPLACED!/xg; 
print $s;

1 !REPLACED!%> 4 <% >% %> 5 <%%%% xxx %%%%> 6