The commonly used Archive::Zip module does not support zip encryption:

The Archive::Zip module does not currently create or extract encrypted members.

Besides the original, and according to wikipedia, seriously flawed PKZIP encryption algorithm, there are apparently differ implementations of zip file encryption:

• WinZip
• 7-Zip
• SecureZIP (aka PKZIP).

I'm unaware of any Perl interfaces to these implementations.

There are a number of good alternatives to the above, try to search cpan or monastery.