The commission's first National Strategic Skills Audit for England ranked agriculture and horticulture 25th out of 27 industries in terms of its future economic significance and third out of 27 in terms of skills deficits.
"I am very disappointed that UKCES has given agriculture and horticulture such low priority," said NFU deputy president Meurig Raymond.
"This is particularly strange given the strategic role farmers and growers have and will play in securing the nation's food security and in feeding a growing global population, while using less natural resource, and reducing agriculture's impact on the environment.
"Portraying the farmers and growers as low-skilled and of low priority could colour consumer opinion and jeopardise future funding for much-needed skills and training, which is crucial if we are to achieve all that is expected of our farmers and growers in the 21st century."
NFU president Peter Kendall also spoke out on the issue, urging government to get behind farming. "For our industry to thrive we need to see farming and growing at the heart of policy-making."