The rise has been postponed until Sept 1, but it will add 1.22p/litre to the cost of agricultural diesel, a rise of 20%.
Bob Howat, vice president of NFU Scotland, said the move would not help to tackle red diesel fraud.
“This simply looks like an attempt to increase revenue. Whilst an increase in the duty may dent fraudsters‘ profits, it doesn’t tackle the problem at its source.
“To do that, the Treasury needs to devote greater resources to enforcement through increased inspections and dipping of vehicles.”
Welsh Union leaders also condemned the rise in road fuel duty. Business development director Emyr James said:
“We are already paying the highest fuel prices in the world thanks to the extortionate level of this stealth tax imposed by the Government.
“We are angry that the Government is failing to listen to the views of drivers and continuing to increase the costs of motoring.
“People living in rural areas are particularly vulnerable to increases in fuel costs because in many cases public transport simply does not exist.”
But he welcomed other elements of the Budget, including the pledge to prune the number of regulatory bodies overseeing agriculture from 22 to five, covering food safety, the countryside, agriculture, animal health and environmental protection.
“Any move to reduce the excessive burden of red tape that can strangle the life out of farm enterprises and other small businesses is to be welcomed,” said Mr James.
“The union particularly welcomes his pledge to halt the trend for ‘gold plating‘ European regulations – the practice that is almost unique in Britain of following every EU rule to the letter.”
The NFU also welcomed the plans, but said that they would have to be carefully worked out so they actually did cut farmers‘ paper burden.
The unions also welcomed the increase in the thresholds for inheritance tax to £300,000 and for Stamp Duty to £120,000.