Akin, who initially lost much Republican support after he said in August rape victims had a natural biological ability to fight off pregnancy if the rape was "legitimate," received support from the National Federation of Independent Business, the federation said.
"In this term, Congressman Akin earned a perfect 100 percent score and has a lifetime NFIB voting record of 97 percent," federation Senior Vice President Lisa Boeas said in a statement Monday.
"Senator McCaskill, on other hand, in this term earned a score of 45 percent and has a lifetime NFIB Voting record of 44 percent," Boeas said.
The 350,000-member federation calls itself non-partisan but has historically contributed almost exclusively to Republican candidates, the non-profit Center for Responsive Politics says. The center tracks the effects of money and lobbying on elections and public policy.
Akin's campaign had no immediate comment on the NFIB endorsement.
The federation's political action committee, the Voice of Free Enterprise, sent out an anti-McCaskill flyer to 16,000 Missouri small-business owners Oct. 8, appealing to them in big block letters to "Vote Against Claire McCaskill."
"Missouri needs jobs, not taxes and regulations," it said.
Akin is not mentioned in the flyer, which was mailed a week before the federation formally endorsed him.
The mailing was first reported by the weekly magazine The Nation.
After making his controversial comments about rape, the six-term congressman came under immediate pressure to quit the race, including from Republican presidential nominee Mitt Romney, Senate Minority Leader Mitch McConnell, R-Ky., and Sen. John Cornyn, R-Texas, chairman of Senate campaign efforts.
Major conservative "super PACs," including American Crossroads and Crossroads GPS, pulled out of Missouri and halted their multimillion-dollar ad campaigns against McCaskill.
Since then, former GOP presidential hopefuls Rick Santorum and Newt Gingrich -- along with Sens. Lindsey Graham, R-S.C., and Jim DeMint, R-S.C., and the Senate Conservatives Fund super PAC -- have thrown their support behind Akin.
McCaskill spent nearly $7 million from July through September in her battle to keep her seat, quarterly disclosure reports her campaign released Monday indicated.
Her campaign still had more than $2.1 million in the bank, the reports showed.
Akin's campaign declined to release its quarterly fundraising totals, but the figures will become available when the Federal Election Commission files reports later this month.
Akin's campaign has said it has raised $1 million in online donations since Akin's rape comment. He has received several hundred thousand dollars in commitments from conservative groups, The New York Times reported.
Independent groups opposing Akin or supporting McCaskill spent more than $3 million on the race as of Saturday, the Times said.
Unseating McCaskill had been viewed by Republicans as one of their best bets in the GOP's strategy to win control of the Senate.