"The problem with the way the sequester was structured is that it actually requires us to look back in time," Vilsack told a group of trade officials Wednesday.
To cope, Vilsack said USDA will pro-rate subsidies to recoup lost funds.
Additionally, the sequester will force conservation reductions, fewer overseas trade promotion efforts and cuts to some rural development programs.
Vilsack said despite all the cuts, the amendment to the Senate CR to fund food safety inspectors acknowledges that USDA has no options under sequester.
"We have no other option, and I sincerely hope that folks recognize this is not a bluff, this is not make-believe, this is real," Vilsack said of the cuts.
The Senate CR will now head to the House of Representatives for a vote, which Congressman Paul Ryan, R-Wis., told Bloomberg was likely to be favorable.
A final vote also frees up the rest of the week to work on the budget proposal offered by the Senate, which offers up savings found in the farm bill.
Last week, the text of the plan was revealed, showing a possible $4.25 trillion in deficit reduction and a projected savings of $23 billion from the Senate Farm Bill.
The Senate plan also focused on programs it plans to retain, including conservation investments and cost-share programs, agriculture research for land-grand universities, and investments in clean energy.
It also offered a safety net program with flexibility for the Senate Agriculture Committee to write a five-year farm bill.
Click here to read full text of the CR.