NFU president Peter Kendall said more than two million tonnes of wheat had been lost because of last year's poor summer.
The prolonged cold weather would also hit this autumn's harvest, he said.
But he said the shortage was unlikely to affect the price of bread because of the global nature of the market.
Speaking on BBC Radio 4's Today programme, Mr Kendall said the average yield fell from 7.8 tonnes a hectare to 6.7 tonnes last summer.
Looking ahead to the 2013 harvest, he said farmers had managed to get only three-quarters of the planned wheat planted this year, so the UK was already 25% down on potential production.
"I've been walking crops yesterday on the farm in Bedfordshire and they look pretty thin. We would normally say you should hide a hare in a crop of wheat in March. You'd struggle to cover a mouse in some of mine.
"If we got three-quarters of the area planted, and the same yield as last year, we could be looking at a crop of only 11m tonnes of wheat when we actually need 14.5m tonnes of wheat for our own domestic use here in the UK," he said.
Andrew Watts, a wheat farmer and the NFU combinable crops board chairman, said farmers had been hoping for a kind autumn after a poor harvest in 2012, but this had not happened.
"It seems many farmers have written 2013 off and are trying to do what they can with the crops in the ground. Everyone is focussing on 2014 and making sure the land is in a good condition to get good crops then.
"This is what producing food is all about - the weather."
He added: "We have got to put it in context, this is only the first time since the late 1970s that we have been net importers, Over the past five or six years we have been in surplus."
The crop damage is dealing a further blow to Britain's farming industry, which is already reeling from a spate of recent livestock deaths due to the cold weather.
But Mr Kendall said only about 10% of the cost of a loaf was attributable to wheat. The rest was due to processing, transport, and packaging, he said.
"We could see wheat double and the impact on a loaf of bread would not be enormous.
"But we need to make sure, in the UK, we are producing raw materials for what has been - despite the weather - a fantastically successful sector," he said.
Britain will become a net importer of wheat for the first time in a decade this year because of bad weather, the National Farmers' Union has said.