No trains are running in Cornwall and Devon has a hugely reduced service on the second day of industrial action.
The first day of strike action took place on Tuesday, and a third walkout is scheduled for Saturday, with talks due to continuing between rail firms and unions.
Dan Panes, from GWR, said: "How the signalling system works in Cornwall is much more complex than the rest of the UK and the GWR patch.
"Our signallers really have to man-mark each individual signal on all those branch lines in Cornwall.
"If we focused the attention there from a Network Rail point of view, we pretty much wouldn't be able to run any services elsewhere."
Mr Panes added: "We have got contingency managers out and about around the network to keep those services that we can run, running.
"But at this late stage, the work that has gone in to prepare the new timetables for this current period, to make sure that we have got the right people in the right place, means that even if the RMT came out today and said the whole thing was off, we would still see some significant disruption over the next couple of days."