The new tariff, effective from July 24, replaced a rate that had been due to expire that day.
NFF chief executive Michael Guerin said the move was a step backwards for two nations with a long agricultural and economic partnership, underpinned by the Australia-US Free Trade Agreement, which provides for zero tariffs on two-way trade.
"Australian agriculture is profoundly disappointed by this announcement," Mr Guerin said.
He said the increase added further challenges for exporters, particularly given other economies faced a lower 10 per cent rate, and came despite Australia's long record of high standards and responsible trade.
While major exports including Australian beef appeared to remain exempt, Mr Guerin said the decision was still a disappointing setback for exporters more broadly.
"Australian farmers are among the least subsidised in the world and have built a global reputation for producing high-quality, sustainable and reliable food and fibre," he said.
The NFF said it remained committed to a measured approach, emphasising open markets and Australia's reputation as a trusted trading partner as the best path forward.
"We will continue working with government and industry to ensure Australia's trade interests are protected and to expand opportunities in markets that value the quality and integrity of Australian agricultural products," Mr Guerin said.
The peak body reiterated its long-standing support for free and fair trade across all industries, citing its importance to global economic growth, stability and food security.
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