Ed Bailey, president of NFU Cymru told the BBC that feed for livestock has been particularly affected.
Wheat crops were hit by the summer rain with yield in England down by almost 15% on the five year average, with productivity down to 1980's levels. Some farmers in the wet western half of England reported even lower yields.
Poor UK harvests also mean smaller fruit and vegetables than normal.
Last summer was the second wettest in the UK since records began, Met Office figures indicated. The only summer - defined as June, July and August - which was wetter since national records began was in 1912. A drought across much of England during the spring followed by record-breaking wet weather has meant a poor wheat harvest for many farmers, the NFU said.