But on Capitol Hill and among lobbyists there was an outpouring of appreciation for Conner's work and some surprise he did not get the nomination.
Questions were raised about how Schafer will fare in final negotiations on the farm bill and whether the Bush administration is positioning Schafer to run against Sen. Byron Dorgan, D-N.D., in 2010.
"I offer my full support to Governor Schafer, confident he will build on the agricultural accomplishments of this administration and advance policies and programs that ensure continued strength in the agricultural economy," Conner said.
Senate Agriculture Chairman Tom Harkin, D-Iowa, congratulated Schafer, but also said he wanted "to thank and commend Chuck Conner for the fine job he has done as acting secretary."
While there had been speculation Southern senators would object to Conner's nomination because he has strongly supported payment limitations that would hit the South hardest, Sen. Blanche Lincoln, D-Ark., said she knew of no such objections.
Lincoln said she was "shocked" that Conner did not get the nomination. "We've been dealing with him the past seven years," she said, adding that she did not think a former governor of North Dakota would be more sensitive to Southern issues than Conner.
Senate Agriculture ranking member Saxby Chambliss, R-Ga., said he was glad Bush had nominated Schafer and did not mention Conner.
One Senate aide said Bush's decision proved that the job of Agriculture secretary "has always been a political position, especially in this administration."
American Farm Bureau Federation President Bob Stallman and National Farmers Union President Tom Buis issued statements congratulating Schafer, but Stallman also praised Conner.
Other lobbyists said Conner deserved the top job, especially since he left a high-paying job at the Corn Refiners Association to become a White House agricultural aide when former Agriculture Secretary Ann Veneman developed a rocky relationship with Congress during consideration of the 2002 farm bill.
One angry lobbyist said Conner "should leave the administration in the middle of the farm bill and take a couple of his top aides with him. The administration would be lost."
Schafer is under pressure to support provisions opposed by the administration that Senate Budget Chairman Kent Conrad, D-N.D., his fellow North Dakotan, has inserted into the Senate bill, which is expected on the floor next week.
Those provisions include increases in the target price and loan rates for wheat and other program crops, the sugar loan rate increase and the permanent disaster bill that Conrad worked on with Finance Chairman Max Baucus, D-Mont.
House Agriculture Chairman Collin Peterson, D-Minn., said in a statement he has known Schafer "for a long time" and has "a good personal and professional relationship with him."
He added, "The question is whether he will have to toe the administration's line or whether he will be able to soften their position on issues like sugar and permanent disaster assistance."
Some lobbyists and Capitol Hill aides noted that if Bush threatens to veto the farm bill over provisions that are popular in North Dakota, Dorgan could use that against Schafer in a 2010 race.
North Dakota Agriculture Commissioner Roger Johnson, an elected Democrat serving as the president of the National Association of State Departments of Agriculture, said in a statement that, "I anticipate Governor Schafer will support North Dakota farm bill priorities to establish a permanent disaster program, re-balance loan rates for northern tier crops, and make investments in farm-based renewable energy."
Dorgan said Schafer had called him to tell him he had been nominated. "I look forward to meeting and visiting with him as he begins the confirmation process here in the Senate," Dorgan said. "I think it's a real honor to have a North Dakotan nominated for a Cabinet position."