Digest::MD5 doesn't take an array; it takes a string.

If simply passing your strings to Digest::MD5::md5() does not produce the same 16-byte value that the Java code is producing, it will be because the Java code is digesting the entire 256-byte packet including the trailing nulls.

Therefore the solution is to pad the string to 256-bytes with nulls before generating the md5:

my $string = ...; # get the string from wherever
$string = pack 'a256', $string; ## Will null pad to the specified leng
+th
my $md5 = md5( $string );
... do the twofish stuff.
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That doesn't deal with strings that start out greater than 256, but neither does the Java code.

It will also not correctly deal with strings where char != byte.

If that is a requirement, the simplest solution will be to turn off the utf flag before the pack, but there is undoubtedly a (suite of) modules that will do the same thing.