Johanns was expected to announce his candidacy as early as Monday for the seat being vacated by fellow Republican Chuck Hagel after two terms. Analysts say Johanns would be the front-runner of four men seeking the GOP nomination.
Nebraska is a Republican-leaning state. Democrats have talked of recruiting Bob Kerrey, a former U.S. senator and Nebraska governor who is now a university president in New York City. Democrats control the Senate, 51-49.
As agriculture secretary, the mild-spoken Johanns pressed U.S. trading partners to remove barriers to U.S. beef, erected out of fears of mad cow disease, and to expand farm exports, which account for a quarter of farm income. He took the lead in administration proposals to deny farm subsidies to the wealthiest Americans.
In his resignation letter to Bush, Johanns said the U.S. farm sector "is stronger than ever before," with high crop prices and record farm exports.
"After careful thought and difficult deliberation, I am writing to inform you that I have decided to pursue a new opportunity to serve this great nation," wrote Johanns.
Nebraska is a major grain and cattle-producing state. Democrats in Nebraska said Johanns was leaving USDA without completing an important task -- overhaul of U.S. farm policy this year.
Johanns resigned as governor to become agriculture secretary in January 2005. Born in Iowa, Johanns practiced law in western Nebraska before election as mayor of Lincoln, the state capital, in 1991 en route to the governorship in 1998. He once said that for a former farm boy, being agriculture secretary was a dream job.
Deputy Agriculture Secretary Charles Conner was named acting secretary until Bush nominates a permanent replacement.
The Agriculture Department, with 100,000 employees, is in charge of crop subsidies, the national forests, a vast research network and public nutrition programs including school lunch and food stamps.
Ferd Hoefner of the Sustainable Agriculture Coalition, said Johanns was the first USDA chief in decades to try to rein in farm payments and to show interest in beginning farmers.
But lawmakers have faulted Johanns for the faltering campaign to create a nationwide animal-tracking system, originally embraced by the administration as a key safeguard against mad cow and other fearsome diseases. USDA relies on voluntary participation in the program.
"He has been a clear and open advocate for ethanol within the administration," said Jay Truitt of the National Cattlemen's Beef Association. Truitt said Johanns "was the first to understand" how the explosive growth of the fuel ethanol industry would squeeze livestock and meat producers.