MPs have warned that the Government's record on dealing with farming subsidies does not bode well for Brexit.
The Commons Public Accounts Committee (PAC) expressed concern at delays in payments to farmers and landowners.
A report into the delivery of Common Agricultural Policy (CAP) payments, and rural development, raised fears over the Government's attitude to farmers after the UK withdraws from the EU.
The probe criticises the Department for Environment, Food, and Rural Affairs (DEFRA) over how it has handled the Basic Payment Scheme, stating: "The department's record of failure when developing systems to support subsidy payments to farmers does not inspire confidence in its ability to cope with the challenges associated with Brexit that lie ahead."
DEFRA gives £1.8 billion a year in CAP payments to English farmers and landowners and the report warns that the Rural Payments Agency (RPA) is failing to deliver money on time.
PAC deputy chairman Richard Bacon said: "The recent history of the Basic Payment Scheme is a sorry affair.
"Farmers have suffered badly from the collapse in service levels and Government has done too little to help them cope with the fallout.
"At the same time, taxpayers continue to be hit in the pocket by financial penalties arising from the Government's failure to deliver the scheme properly, penalties running to more than half a billion pounds for England in the current period.
"Rapid and effective change is required during what is a critical phase for the Rural Payments Agency, whose chief executive is leaving at the end of this month, and the Department for Environment, Food and Rural Affairs more widely.
"If farmers are to be properly supported through Brexit and beyond, it is vital their interests are represented at senior level. In particular, the RPA must be at the table during discussions of any future subsidy payment scheme."
The report states the Government must move to better understand the impact of late payments and learn the lessons from the floods of 2015 "to ensure payments to farmers in times of crisis are not delayed".
The committee found that RPA paid only 38% of farmers under the Basic Payment Scheme on December 1 2015, the first day of the payment window, compared with more than 90% in previous years. By the end of January last year, that had climbed to 76%, but at the end of March, there were still 14,300 farmers, 16%, who had not received any payment.
More than 10,000 farmers who had received a payment had not been paid in full. Two thirds of the additional payments made to these farmers were in excess of 1,000 euros and were first paid in September last year, more than nine months after the first monies could have been received.
The report states: "Many farmers who did not receive their payment in a timely manner were forced to seek alternative means of funding. Some had to sell livestock to meet their financial obligations."
A Defra spokesman said: "The CAP is a complex and bureaucratic scheme. The UK Government is working to improve the system and ensure farmers get the support they are entitled to.
"We have made major progress - this year the Rural Payments Agency has already met its target to pay 93% of farmers by March 2017, and it is working hard to get outstanding payments into bank accounts.
"We are leaving the European Union. This represents one of many opportunities to design a better system which supports farmers and our agricultural economy and cut unnecessary red tape."