Plugin timesout

I have a custom plugin that allows users to 'clone' a project and it's configuration, as this takes sometime to run whilst it copies the project, the configurations, the VCS roots, makes changes and applies Roles to users, sometime the script appears to timeout displaying:

HTTP Status 404 - /error/HTTP_BAD_GATEWAY.html.var

type Status report

message /error/HTTP_BAD_GATEWAY.html.var

description The requested resource (/error/HTTP_BAD_GATEWAY.html.var) is not available.

Apache

Is there something that I need to do to for it to stay alive?

Many thanks, Simon