Hi,
I assume you are using a GPIB interface with a TNT488 IC. If that is the case, here's the user manual of this IC:
http://digital.ni.com/manuals.nsf/websearch/91aaba0122b5f7168625665e00691c89?opendocument
The following link contains all the register level programming resources:
http://www.ni.com/support/gpib/reg_prog.htm
I don't know if the handshake can be disabled, but you can check the user manual to check.
DiegoF.