Affco was charged with failing to ensure workplace safety under the the Health and Safety in Employment Act.
"While Affco had taken some steps to mitigate the risk of falling by installing the gate and fall arrest safety harness, the fact is that these measures were neither managed well nor were they adequate at any time," said MBIE Labour Group general manager, John Howard.
"No employee goes to work to be injured. The onus is on the employer to ensure employees are not exposed to harm and potential injury - and in this case the injuries were significant.
"Today's decision sends a clear message to Affco that it needs to both understand the responsibility it holds to its employees and deliver on it," said Mr Howard.
Affco Horotiu Operations Director, Rowan Ogg said the fine was "in the area that we anticipated".
He said although the safety mechanisms were there, they weren't failsafe. Although a harness was provided, it did not necessarily mean that the employee was using it.
Mr Ogg said following the accident an independent safety audit was commissioned across all Affco plants, and as a result the shaft has been rendered inoperable unless safety mechanisms are in place.
"The mechanism is now failsafe."
Mr Ogg did not comment on whether any Affco employees faced disciplinary action following the incident, and said it was an "internal matter".
The injured employee is still employed by Affco.