How can I implement the Unix "cksum" command in Java?

cksum uses the CRC-16 algorithm, not the CRC-32 algorithm. You need to use another implementation of the Checksum interface for this purpose - it's easy to write your own or find someone else's code. Here's one, for example: http://www.mcmanis.com/~cmcmanis/java/encoders/index.html.