Since the Pike River mine disaster about eight years ago a lot more attention has been paid to the safety risks of operating trains through long tunnels. Some particular examples of changes have been the need to have fire suppression fitted to locomotives hauling trains through these tunnels, and extra locomotives required where necessary on the trains as well.
An example that shows just how much change has happened in recent years can be seen from the comparison with the report into a locomotive fire in the Rimutaka Tunnel in 1995. The locomotive was hauling a passenger excursion from Wellington to Featherston and the fire was discovered while uphill from Upper Hutt in the tunnel. The action taken was to keep running the engine until the summit in the tunnel was reached, then shut down the locomotive and coast downhill towards Featherston.
The TAIC report is number 95-104 and can be found here. What I found astonishing was that it was considered acceptable to have no radio comms in the tunnel. The second much more serious issue that was not even acknowledged by TAIC was the risk of the train running away through lack of braking capacity. With the locomotive shut down there is no dynamic braking available, and the air supply from the locomotive will eventually run out if the air brakes are used, as they must have been in this case.
This is probably some of the reason why passenger trains through the Otira Tunnel now have to have a locomotive at the rear as well as at the front.