First Great Western Trains say that one of their drivers suffered serious cuts and bruises to his face after an object the size of a brick was thrown from a bridge.
The 'rock' smashed through the driver's window as the train made its way from Romsey to Salisbury.
The Portsmouth to Cardiff service was delayed by an hour. A doctor on board the train treated the injured driver and a South West Trains driver stepped in to take the locamotive to Salisbury.
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The video, obtained by ITV News, shows scores of migrants desperately trying to board lorries in a restricted area within the tunnel.