South West Trains said that all services had been brought to a halt by the incident.
The company say they were briefly stopped and were now normal.
Thousands of passengers would have been on trains on that section of line at the height of the rush hour.
Some rail passengers from the south heading to London have been delayed after a helicopter crashed into a crane near Vauxhall in south London.
The incident which is being classed as a major emergency happened just after 8am.
All trains from the south to Waterloo pass near where the incident occoured.
Services were stopped because of heavy smoke.
South West Trains say services are now running as normal and current delays are minimal.