Party agriculture spokesman David Carter said information released under the Official Information Act showed PPCS (now Silver Fern Farms) and Alliance killed 17,000 cull ewes for Landcorp during an exceptionally dry March, when many farmers were unable to get space.
"This favourable treatment was happening as I was receiving calls from desperate farmers through February, March and April, who had their cull ewes booked for processing for months."
But Silver Fern Farms and Alliance have dismissed his claims, saying space was allocated based on loyalty of supply.
Alliance chief executive Grant Cuff said Landcorp traditionally supplied lambs from October to May, and this year's supply profile was no different.
Mr Cuff said Mr Carter's supply history was an example of how Alliance favoured regular and loyal suppliers.
He said the MP-farmer had not supplied ewes to Alliance for two years until this year, when he quit 300 ewes, but had to wait his turn for killing space.
"We believe we have tried to be equitable with all farmers, including Landcorp, but not to Landcorp's advantage. Those people who believe they have been most disadvantaged are likely to be those with an inconsistent supply history," he said.
Silver Fern Farms chief executive Keith Cooper agreed, saying space was allocated based on supply history across all animal species.
Companies other than the two co-operatives also processed Landcorp stock.
Mr Carter's figures reveal Landcorp killed 52,000 cast for age ewes with the two co-operatives between December and April 30, with 29,000 of those killed by Silver Fern Farms and 22,000 through Alliance.
Nearly half the ewes, 24,400, were killed from the start of March to mid-April.
Mr Carter's main concern was that most were killed from late January when conditions were getting dry and farmers were desperate to quit stock to conserve feed.
