The ceremony for the Trade Association Best Practice Awards was held in London on 24 July.
The union also picked up awards for best Environment Initiative and Magazine of the Year for British Farmer and Grower.
The judges were impressed with the NFU’s approach to last year’s floods, avian flu, the foot-and-mouth outbreak and bluetongue.
The judges said the NFU responded with leadership to crisis after crisis, both as a voice and lobbyist for the industry.
NFU director of communications Liz Falkingham said: “The NFU is delighted to have won these awards.
“This is recognition of the superb work and dedication of our staff and members and it is particularly special to win in this our centenary year.”
The CBI Trade Association Best Practice Awards, were launched in 2002 to recognise and reward the achievements of Trade Association Forum members. The rewards are held in high regard, with nearly 170 entries submitted this year.