The program had targeted wolves near where livestock and pets were being killed and had the approval of farmers, conservation leaders, wolf lovers, natural resource officials and politicians of both parties, the Duluth News Tribune reported.
But a moratorium on earmarks in Washington means there's no money for the program after fiscal 2011 ends Friday, the newspaper said.
In the past, congressional members from Minnesota and Wisconsin had routinely used earmarks get funding for the program.
"We've got too many wolves causing too many problems now," Dale Lueck, treasurer of the Minnesota Cattlemen's Association, said.
"But if you take this program away, it will be a disaster. Starting Oct. 1 you're going to make law-abiding Minnesotans guilty of a federal felony offense when they go out to protect their own livelihood."
Even wildlife advocates said they were in favor of the program.
"We're losing one of the best wolf conservation tools we've had. It was so effective at solving the problem without randomly harming wolves," Nancy Gibson of the Minnesota-based International Wolf Center said. "And there was such an educational element. The trappers had so much expertise, I think they really helped the farmers avoid problems."