The Rural Payments Agency says it has now informed all farmers unlikely to receive their Single Payment this month.
Payments totalling some £1.16 billion have been made to 85,060 farmers (80.6%) in England with the last few weeks, according to agency figures.
But that leaves about 20,000 farmers still waiting to receive their money.
The agency said it would continue to strive to meet its target to pay 85% of eligible claimants by the end of December.
There were different reasons why some farmers would receive payments earlier than others, said an agency spokeswoman.
Some cases were more complicated and took longer to process than others which were more straightforward.
Reasons for later payment could include entitlement correction work and inspections carried out under EU anti-fraud rules.
There were also some probate cases and others where the agency was still waiting for partnership or bank details from the farmer.
“Significant numbers of farmers have been paid in the first few days of the seven-month payment window,” the spokeswoman said.
“This leaves others wondering why they have not been paid yet.”
The agency was committed to improve its communications to farmers, the spokeswoman added.
This was why it had written to those farmers who were unlikely to be paid before the end of December to keep them informed.
One farmer who faces a longer wait is Farmers Weekly Farmer Focus writer Charlie Armstrong, who farms at Alnwick, Northumberland.
He has been sent a letter informing him that the agency is checking his entitlement payment.
Mr Armstrong said he had been told he wouldn’t receive anything until March.
Other farmers in the area have also received the same letter, he said.
In a normal year, Mr Armstrong said he would be able to cope with the cash flow disruption caused by the late payment.
But he fears he will struggle this year due to severe winter weather. Earlier this month, more than 30cm of snow fell in less than 24 hours.
Unforeseen expenses included buying in extra feed and making right a livestock shed that had collapsed due to the weight of snow.
NFU single payment adviser Richard Wordsworth said the letters would come as a shock to some farmers.
The agency was trying to deal with complicated claims once and for all, rather than letting them drag on for another year, he said.
“We don’t have any problem with the RPA trying to get claims right and robustly sorted out,” he said.
“The difficulty people have is simply that their cash flow won’t stand an uncertain period and delay in receiving money much past January.”