American farmers are supportive of President Donald Trump, despite feeling the pain from the escalating tariffs between the U.S. and China, Agriculture Secretary Sonny Perdue told CNBC on Wednesday.

"They understand what the president's goal is. They've been amazingly supportive through this period of time, even under financial duress," he said on "Closing Bell."

When asked how long the pain was expected to last, he replied, "It's like a drought. We don't know. We hope it rains soon."

Trump's latest round of tariffs on $200 billion of Chinese imported goods went into effect on Monday. Beijing retaliated by slapping duties on about $60 billion worth of U.S. imports.

In an effort to help farmers who have been harmed by the retaliatory tariffs, the U.S. Department of Agriculture has authorized up to $12 billion in aid.

Perdue said checks have already started being cut as part of the $4.7 billion in relief for agricultural producers of seven commodities. Soybean producers have been particularly hard hit.

"It's going to be based on actual production so they have to come in and indicate and register their production and it's based on the amount per bushel," he said.

Nearly $20 billion in U.S. agricultural exports went to China last year.

Perdue is hoping a "domino effect" will resolve the issue.

Now that there appears to be a U.S. deal with Mexico, expected to be released on Friday, hopefully Canada will join into it soon, he said. Then there can be talks with the European Union and Japan, he added.

"Hopefully China will see that we will not be intimated into breaking on this and they need to reform their way of doing business," Perdue said.

Earlier this week, China published a 71-page paper accusing the Trump administration of "trade bullyism practices" that have become "the greatest source of uncertainty and risk for the recovery of the global economy."

— CNBC's Jeff Daniels and Yen Nee Lee contributed to this report.