Up to 40,000 farmers were last night facing financial penalties for failing to make the deadline for applications for new EU subsidies.
The cut-off date for applications to the Rural Payment Agency for the new single payment subsidy was midnight last night.
A spokeswoman for the Agency said a total of 140,000 application packs had been sent out and 100,000 had been received by yesterday morning.
Applications will continue to be accepted until June 10 but farmers will have four per cent wiped off their grant for every day it is late.
The National Farmers' Union has criticised the RPA's " shambolic" system for processing the claims.
The new system is the biggest change in UK agriculture in the last 30 years, according to the RPA.
It replaces most of the old subsidy regimes, aiming to free up farmers to produce what the market wants while also rewarding them for looking after the countryside.
Union president Tim Bennett criticised the RPA's handling of the claims.
"Frankly they have had going on for two years to get this process in place. Because of their poor administration there are bound to be errors on some of the forms that have gone in. They could have done a lot better," he said.
Mr Bennett said the system appeared to have worked better in Wales and Scotland, where applications were handled by the Welsh Assembly and the Scottish Executive.
An RPA spokesman said extra staff had been drafted in to help speed up the application process.
Drop-in centres across England were manned over the weekend to cope with the eleventh-hour influx of forms and about 40,000 forms were handed in over the period.
"The response by farmers has been typical in terms of what we have seen in previous years for applications subsidy schemes," said the spokesman.
"The whole point of this exercise is to make it simpler, having just one payment instead of land and animal schemes. Lots of producers are not used to the form."