Vital research into avian flu, environmental pollution and food safety could be reduced to save money, government scientists have claimed.
The Department of Food and Rural Affairs (Defra) has to save £200m partly due to mistakes at the Rural Payments Agency, said Farming Today.
The union Prospect told the BBC Radio 4 programme its members could be forced out of work as a result of the cuts.
Defra said ministers were still working on the budget and would not speculate.
Target for cuts
Farming Today's Anna Hill said Defra's shortfall was due in part to "costly mistakes at the Rural Payments Agency (RPA), which failed to deliver a new subsidy system to farmers on time".
The agency had been criticised for late payments of the new subsidy, which gives farmers a single sum irrespective of how much food they produce.
Some 2,000 farmers were then overpaid by £20m this summer, for which Defra apologised.
Some cheques were stopped, while the agency said it would contact other farmers about recovering the money.
Defra has to save the money in the next six months and government scientists believe they could be the target for cuts.
Prospect told Farming Today public health could be affected if research was reduced.
The union is due to launch a campaign to highlight its concerns.
Defra said until the budget was finalised, it would be premature to speculate on its potential effects.
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