Farming minister Lord Whitty confirmed that new lower payment rates for animals disposed of under the Livestock Welfare (Disposal) Scheme would apply from Tuesday.
The scheme was set up in March to encourage the disposal of animals whose welfare was compromised by the movement restrictions imposed to control foot-and-mouth disease.
Lord Whitty also announced that pork exports to Europe can finally resume from Tuesday after procedures designed to prevent any future outbreak of foot-and-mouth disease were finalised.
The peer confirmed that mass culling would remain the government's policy in the event of a further outbreak of foot-and-mouth, despite the experience of this year's epidemic.
He told BBC Radio 4's Farming Today: "Policy at the moment would be to follow the successful dimensions of the strategy we have adopted so far, which is basically that the culling, as long as we match the target figures, is effective in containing the disease."
On Monday the minister rejected criticism that handling of the crisis in Devon by the Department for Environment, Food and Rural Affairs' (Defra) was "lamentable".
Responding to the findings of the first independent inquiry into the crisis, Lord Whitty argued that the government had been faced with an unprecedented situation.
On Tuesday, Defra said the new scales included lower payments for most categories of animal "to reflect market trends", as well as higher rates for breeding ewes.
But National Farmers' Union president Ben Gill said the decision would hit thousands of vulnerable farmers.
He said: "The whole industry united to condemn these cuts. But these pleas have simply been ignored.
"That Defra has gone ahead, knowing full well the desperate impact this will have on producers with a long winter ahead, shows a heartless and brutal disregard for the state of thousands of farmers.
"This hits the most vulnerable group of farmers who have been under restriction the longest and still cannot benefit from the movement flexibility granted so far."
Flat rates
From Tuesday, there will be new flat rates in compensation, including £350 for breeding cows and heifers, and £30 per head for breeding ewes.
The scheme is due to end on 31 December.
On pork exports, only pigs from areas which have either never had foot-and-mouth or have remained free of the disease for 90 days up to 24 October are eligible for slaughter and for export.
Farmers can now apply to their local authority for a licence to transport pigs to slaughterhouses approved by the Defra.
A ban on pig exports had been in force since the foot-and-mouth outbreak started in February.