"Everybody wants trade, not aid," Perdue said in a "Squawk Box" interview.
"There's not a farmer in America that would rather not have a good crop and a fair price than a government check," he added. "That's what they do. That's what they put their equity on the line every year for."
But since those trade disputes, especially with China, are not settled, the Trump administration is initially making $6 billion available in emergency aid to farmers, starting right after Labor Day.
The Agriculture Department has authorized up to $12 billion in relief to U.S. growers.
Soybean producers, in particular, have been hard hit by Chinese retaliatory tariffs and stand to get up to $3.6 billion in assistance under the Market Facilitation Program.
Trump is pursuing new trade deals and concessions from China and other nations to change what he sees as unfair trading practices.
In June, Perdue told CNBC that Trump instructed him to make a plan for any potential impact from a trade war on farmers.
Perdue said at the time that he was calculating the effects of trade disruptions on a weekly basis and making them known to the administration.
The payments to farmers will be based on "actual production ... not on any kind of average," Perdue said Wednesday. "It's going to be individual, by farmer."
The relief will not be able to make farmers "whole," but to ensure they don't have a disastrous season, he said.
Trump said Monday's trade agreement between the U.S. and Mexico, paving the way to replace the 1994 North American Free Trade Agreement, will help farmers and manufacturers.
Perdue predicted Wednesday on CNBC that the U.S.-Mexico trade deal will get Canada to come along on a finalized, new NAFTA-type agreement among the three nations.
— CNBC's Jeff Daniels contributed to this report.