He was rushed to Christchurch Hospital with serious leg injuries. An emergency operation to save his left leg was unsuccessful and it was later amputated below the knee.
WorkSafe investigated the accident and decided not to prosecute.
However, the New Zealand Transport Agency (NZTA) also investigated and did decide to prosecute Thomson's employers KiwiRail Holdings Ltd and the local contractor MBD Contracting Ltd under the Railways Act. They were charged with failing to take reasonable, practicable steps to prevent the accident.
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Christchurch District Court heard today that both companies, which had earlier pleaded guilty, face hefty fines over the accident.
KiwiRail has already paid $95,000 in compensation to their worker.
Judge Stephen O'Driscoll heard submissions from lawyers for both companies today.
The judge also heard from Thomson himself, who described how the accident has drastically changed his life.
Everyday activities – walking with his wife on the beach, shopping, renovating his house, whitebaiting – are either severely hampered now, or unable to be done at all.
And although KiwiRail has given him an office role at its Greymouth depot, he misses his old job.
"It hurts every day to see the trucks going out in the morning to do the track work and wishing I was out there with the guys," said Thomson who became emotional while reading out his victim impact statement.
His permanent disability has knocked his self-confidence left him self-conscious of his prosthetic leg.
Although he accepts his life has changed and will never be the same, every night when he removes his prosthetic, he asks himself, "Why me?"
Thomson said it's been a "long, hard recovery" and although he's not angry with KiwiRail, he's disappointed that the right things were not in place to prevent the accident.
However, he said he believes KiwiRail is going in the right direction to be able to keep everyone safe.
NZTA prosecutor Sam McMullan said there were failures over ensuring the safety of workers that day, including those issued around exclusion zones, visibility, and communication. The excavator should also have had sensors or alarms for reversing.
Judge O'Driscoll reserved his decision.