Fewer than a third of landowners have applied for new Government grants despite the deadline being less than a week away.
Many will face severe reductions in payments if they fail to apply for the Single Payment Scheme by May 16, the Rural Payments Agency warned yesterday.
The RPA said 30 per cent of applications had been received for the grant scheme, which has been introduced as part of Common Agricultural Policy reforms.
Under the reforms, farmers will be paid for the amount of land they have rather than the amount of food they produce.
Johnston McNeill, chief executive of the RPA, said: "We have had 40,000 applications returned so far out of a possible 170,000 which were sent out.
"Some may be duplicated but we are expecting about 145,000 to 150,000 to come back. This is the year when we will be establishing the amount of entitlements so if they don't come in on time it will be very difficult to establish how many will require payments."
The RPA has a pot of £2 billion to distribute to farmers once they have applied for entitlements and the amount each will receive will depend on the number of applicants.
Applicants who miss the deadline face reductions of four per cent per working day from their payments, and applications received after June 10 will miss out completely.
No entitlements will be allocated after that date for the entire period of the scheme.
Mr McNeill said: "This really is the last call for applicants and we urge anyone planning to submit an application to do so as soon as possible, ensuring they have completed and signed all relevant sections and initialled and dated any corrections."
The RPA has employed extra staff to deal with requests to make changes to the Land Register.
"We have had a lot of new customers, people with paddocks for example, who have wanted to declare land. We expect 10,000 changes to the Land Register each year and this year we have had 35,000."
Mr McNeill added those people wishing to include extra pieces of land should do so on their application form.
"We know that farmers do tend to leave these things to the last minute, but the fact that this is a new scheme means it is important that they do send it now. If everyone leaves it to the last minute it will put us under some pressure."
The scheme replaced most existing crop and livestock payments from January 1 this year.
The Single Payment Scheme calls on farmers to demonstrate that they are keeping their land in good agricultural and environmental condition.
Farmers need to comply with a number of legal requirements relating to the environment, public and plant health and animal health and welfare.