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Silver Fern Farms confirmed staff at the Te Aroha plant were docked two cattle from their daily quota - the equivalent of between 98c and $1.60 for each worker - after downing tools.
The two minutes' silence was requested by Prime Minister John Key and observed by thousands of New Zealand workers.
It marked the start of the official memorial service in Greymouth on December 2.
The pay cut has angered workers, some of whom have since lost their jobs because of a fire at the plant on December 4.
"It's bloody rough, that's how bloody miserable they are," said one upset worker, who did not want to be named.
"They wrote it on the board that we would be stopping at 2pm to pay our respects.
"The chain stopped. We didn't expect to be docked though."
Staff are paid for each beast they process and have a daily quota of 280 cattle. It takes about 63 seconds to skin, gut and bone an animal. Depending on their experience, a worker gets paid between 49c and 80c for each beast processed.
The two minutes' silence meant they would only get through 278 beasts each and that is all they would be paid for.
The worker said the loss of pay was a "kick to the teeth".
"Two cattle, 49c each, that's less than a dollar. What's a dollar to those mongrels."
Silver Fern Farms chief executive Keith Cooper said in a statement all workers were encouraged to observe the two minutes' silence.
He said the local branch of the New Zealand Meat Workers Union approached Silver Fern Farms in support of observing the memorial silence.
"As the meat workers are remunerated on the basis of throughput, Silver Fern Farms offered the union the opportunity for workers to process the missed two animals at the end of day as overtime.
"However, the union declined the offer as a gesture of solidarity with Silver Fern Farms as an employer and in the spirit of comradeship with the West Coast workers."
About 170 workers were thought to be affected.
Union president Mike Nahu said the local union representative declined the offer because the organisation did not want their tribute to the miners to be based on money.
"We chose not to make up the loss. It wasn't about the money, it was about respect."
He could not say if the local union representative explained the decision to all the workers before the stoppage.
Engineering, Printing and Manufacturing Union president Andrew Little said he accepted meat workers were paid on a per-beast processed basis, but thought the company should have paid the workers regardless.
"If Silver Fern Farms don't understand that workers share a bond of solidarity and they are going to punish them for it, that reflects really poorly on Silver Fern Farms. It's an absolute disgrace."
Another Silver Fern worker yesterday said the loss of pay was raised at a meeting after the fire.
"There were quite a few people [annoyed] about it ..." he said. "They didn't know they were not going to get paid for it."
New Zealand Council of Trade Unions president Helen Kelly called the situation "extraordinary".
"I don't think you'll find another worker in New Zealand who had their pay docked for taking two minutes' silence."
Of about 300 workers without work because of the fire, many took jobs at other New Zealand plants.