Lord Haskins said the bad weather, which has left farmers facing multimillion-pound losses as waterlogged wheatfields are written off, could cause more damage to the industry than the foot and mouth epidemic in 2001.
With farmers expected to lose £100 for each acre under grain, some experts estimate the overall cost could top £1bn.
The Guardian this week highlighted the plight of farmers in the north facing financial ruin after abandoning both oil seed rape crops and cereals such as wheat.
Paul Ibbott, the chief arable adviser of the National Farmers' union (NFU), said barely a third of the wheat crop had been harvested at a time of year when farmers should be clearing fields to prepare for seeding. "It will be very serious if we get to September without much harvesting," he added. "Farmers will be facing severe financial problems, and in some cases face going to the wall."
Lord Haskins, who has farmed in East Yorkshire for 30 years, claimed arable farmers were potentially facing worse problems than livestock farmers had during the foot and mouth crisis because no compensation is available for crops that are written off.
The seven-month foot and mouth outbreak in 2001 led to the slaughter of more than 6m animals and cost the taxpayer more than £3bn.
"During the foot and mouth epidemic, farmers were more than adequately compensated and made money out of it," added Lord Haskins.
"But no government is going to compensate for the vagaries of the weather, nor should they. Having said that, this is the worst harvest I have known in my farming years."
He claimed that, in many respects, ground conditions were similar to the 1845 potato blight in Ireland - "high humidity alongside a lot of rain". Worryingly, blight is now appearing on the potato crop in parts of Britain for the first time in many years.
In the north, farmers are being forced to extend overdrafts with empty grain stores, combine harvesters unable to reach sodden fields - and the prospect of low prices for a poor crop if it ever gets to market. Some say it will be cheaper to abandon fields rather than accept rock-bottom prices.
With the EU's reformed common agricultural policy due to be introduced next January, with the aim of "decoupling" subsidies from production to prevent oversupply, Lord Haskins predicted that some arable farmers would consider moving out of cereals altogether.
While some fields would be "set aside" and taken out of production, others would be devoted to grass for raising more livestock.
Both the NFU and the Department of Environment, Food and Rural Affairs (Defra) are considering how farmers - particularly in north-east England, the worst affected area - can be helped through the crisis.
One idea is to coordinate a mutual aid scheme, under which farmers in eastern England and the south who have harvested can help others in the north unable to enter waterlogged fields.
An NFU spokesman said: "We are looking to facilitate any way for those farmers who have harvested to help those who have not.
"We are also exploring, with Defra, the possibility of bringing forward assisted payments that farmers would normally receive throughout the year to cover the current difficulties."
Defra acknowledged that while the harvest was "one of the wettest and slowest on record" it would take several weeks to assess the scale of the problem: "We share the concerns of farmers and, like them, we are hoping for a spell of sunny weather."