Thanks for all the suggestions. The pipe is plastic, the type that comes on a big roll.
I've considered most of the mechanical ways of cleaning it and dismissed them. Feeding a string or rope down a quarter kilometre of pipe just isn't going to happen. If something got stuck in the pipe it would be a nightmare to get out. The connectors haven't been opened in 9 years and are all hidden under the bushes that have grown over the pipe.
I figured that other people must have come up against this problem before so I tried phoning a few people who install hydros and windmills in this area and eventually got to speak to someone who had dealt with it, he said he first tried putting a rope down the pipe but gave up on it and ended up filling the pipe with dilute caustic soda (sodium hydroxide) and left it overnight, said it worked great.
As for filtering, a large settling tank would do it but it would be very difficult to construct where the inlet is high up in the mountain, the stream is in the bottom of a narrow rocky gorge so getting materials there would be real challenge.
Thanks Chris, I'll talk to Bob.