Lusk said Alliance appeared not to fit the eligibility criteria for the wage subsidy.
"The wage subsidy was for companies had an actual or projected fall in revenue of more than 30 per cent. They were an essential service that continued to operate during the lockdown.
"They either have a fall in revenue of more than 30 per cent in which case they are entitled to keep the entire amount - or they have not had a fall in revenue of more than 30 per cent and they should pay back the entire amount.
"There is no criteria where you can pick and choose how much of the subsidy you keep.
"They may be able to justify doing so (part repayment), but they may not and it is important that an impartial referee (the court) adjudicates."
Alliance chairman Taggart has said Lusk's court filing is "spurious and unfounded".
"Alliance Group predominantly processes sheep and the nature of our processing means we were more severely affected by the Covid-19 operating restrictions than other companies," he said.
Taggart said the company had been open and upfront about the wage subsidy.
"We have been in ongoing discussions with the Ministry of Social Development about the application of the subsidy and stated from the outset that we would return any funds not used to pay people. In line with that commitment, we have returned $17 million of the subsidy."
Alliance wasn't the only meat company to claim large wage subsidies.
The taxpayer-funded subsidy programme paid around $111m to meat companies, a sector deemed an essential service and allowed to keep working in lockdown.
The meat industry reported record export sales this year.
The largest meat company claimants were Silver Fern Farms, paid $43.2m for 6161 employees, Alliance Group, which received $34.3m for 4913 staff, and the Anzco group of companies which got $17.3m for 2478 employees.
Silver Fern Farms repaid the subsidy in full in July.
Herald inquiries suggest the wage subsidy was claimed for around 13,500 of the meat industry's estimated 22,000 employees.
Several smaller meat companies also claimed the subsidy.
But some large industry players did not. They included Affco, Greenlea and Hellaby, which between them employ more than 6000 people.
Alliance posted a before-tax profit of $20.7m for FY19. Silver Fern Farms, half owned by Shanghai Maling (Hong Kong) and half by a New Zealand farmer co-operative, announced a $70m net profit for FY19. Japanese-owned Anzco posted record revenue of $1.7b and a net profit after tax of $22m. Operating cashflow was $140.7m.
Chairman Taggart is elected by Alliance farmers and has been on the board since 2010.
Independents Brown, Milne and Schuyt joined in 2018, 2013 and 2017 respectively.