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The farmer-owned meat processor had already repaid $21 million of the $34m wage subsidy and will return the balance, it said.
"From the outset, Alliance has been clear we would only use the wage subsidy in the way it was intended by government and our previous repayments reflect this commitment," chairman Murray Taggart said in a statement.
"Following the filing of our company accounts last month, the Alliance board believes the co-operative is in a position to repay the remaining balance," he said.
"We acknowledge the support and certainty the government provided to help us keep many of our people in jobs."
Separate to the wage subsidy, the co-operative has retained $1.9m for the Leave Support Scheme payment to employees that were required to self-isolate or were unable to work, Taggart said.
Self-styled professional campaigner Simon Lusk in September sought to bring a private prosecution against Alliance for its failure to completely repay the subsidy.
Earlier this year, Alliance's Dunedin-based rival, Silver Fern Farms, paid back its $43.3m wage subsidy and declared a $12.4m dividend.
Alliance's move follows a growing list of major corporates to repay the subsidy.
This week, NZX-listed retail giant, The Warehouse said it would repay $68m in wage subsidies received from the Government.