The processor, which is quitting the sector, believes it is entitled to 90% of the E145m fund. However, the government plans to give 30% to growers and machinery suppliers, and only 70% to Greencore, which has been granted High Court leave to seek a judicial review.
In its latest interim results, Greencore wrote off the estimated E44m cost of exiting the industry - based on the belief that it would receive E131m in compensation.
A Greencore spokesman said: "The company is confident that its entitlement to 90% of the aid will be upheld by the court. The interim statements were clear about the financial consequences of Greencore not receiving its full entitlement."