Barnaby Joyce has moved to return a $40,000 cheque handed to him by mining magnate Gina Rinehart on Tuesday night, a cash award described as "very unusual and concerning" by Opposition Leader Bill Shorten.

Mr Joyce took time out from campaigning in the New England byelection to attend an agricultural sector event where Ms Rinehart, a long-time supporter, presented him with the inaugural award and labelled him a "champion of our industry".

The National Farmers' Federation, which was involved in organising the National Agriculture Day event, has quickly distanced itself from the cash prize. President Fiona Simson said the organisation was not consulted and "completely surprised" by it.

Labor questioned why Ms Rinehart would award the prize and why the former deputy prime minister and agriculture minister would accept the cheque in the first place.