Environment department staff should not be getting record bonuses while farmers face long delays to payments, Liberal Democrat Chris Huhne says.
Farmers are facing long delays in EU payments
The Lib Dem environment spokesman said performance bonuses worth £4,296,268 this financial year - up 27% on the previous year - were "astonishing".
Ministers have admitted not all farmers will get full EU payments on time.
The government said the bonus figures were for the whole department, not just for staff dealing with farm payments.
'Record of failure'
The bonus amounts emerged as ministers confirmed that there will be problems with getting the money to farmers for a second successive year.
The government's Rural Payments Agency (RPA) allocates about £1.5bn under the EU's single farm payment scheme.
Partial payments will be made to farmers to help with the shortfall they face.
Mr Huhne told BBC Radio 4's Today programme: "There is an extraordinary record of failure in this area.
"The idea that we should be paying a larger performance bonus for what is a failing department seems to me to be quite astonishing."
But a Department for the Environment, Food and Rural Affairs spokesman said the bonuses had been "not just for people in the RPA, but for people right across the department".
He added: "The element that Mr Huhne thinks is failing is an executive agency of the department. We deal with many different directorates."
Farmers claim long delays in payouts have driven them to take out loans and forced some into bankruptcy.
Environment Secretary David Miliband said the latest estimate for this year was that 99.2% of payments had been made, more than 110,000 farmers had received the full amount and a further 4,756 a partial payment.
The Conservatives urged the government to ensure farmers receive their money by Christmas.