Farm leaders have pledged to work with Defra to ensure support payments are properly administered after the department saw its budget cut.
Defra has been told to make £83m of “efficiency savings” under government plans to slash public spending by £3bn.
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It comes days before the deadline for Basic Payment Scheme applications on 15 June.
Treasury chief secretary Greg Hands wrote to government departments on 20 May, asking them to identify savings and achieve underspends this year.
Savings for 2015-16 will be achieved through further efficiency savings, tighter control of budgets to drive underspends and driving through asset sales, said the Treasury.
Although the cuts are unlikely to have an immediate effect, industry leaders fear they could affect the way farm payments are administered.
The Rural Payments Agency, which is a Defra body, is expected to oversee some 86,000 farm payment applications this year alone.
At the same time, it must get to grips with a new payment system under the reformed CAP.
The Country Land and Business Association said it would work closely with Defra officials to help the department achieve its goals.
CLA president Henry Robinson said: “Defra is an important department that does crucial work to create a regulatory framework that is a vital factor in how rural businesses make decisions.
“It also plays an essential role in administering support payments. We will work closely with officials to help them understand how they can achieve their objectives.”
Priority work included administering basic payments, tackling animal and plant disease and ensuring regulatory enforcement was efficient and targeted, said Mr Robinson.
The government said Whitehall departments had found a further £3bn savings this financial year – equivalent to about 3% of unprotected departmental spending this year.
Chancellor George Osborne said: “Reducing the deficit – that is how you deliver lasting economic security for working people.
“For as everyone knows, when it comes to living within your means, the sooner you start, the smoother the ride.”