The Institute of Cancer Research rejected the money on the grounds that it "recognises the necessity of minimising pain and suffering in animals".
But Britain's two biggest cancer charities said this week they would have accepted the money from field sports enthusiast Barry Atkinson, who organised fundraising shoots over 148 consecutive days.
Cancer Research UK, which accepted a donation from Atkinson last year, said in a statement: "As Mr Atkinson's fundraising was carried out by legal means, the charity would accept funds he decides to donate to our work."
Peter Cardy, chief executive of Macmillan Cancer Relief, said his organisation only refused gifts from sources that opposed the interests of beneficiaries - tobacco companies, for example.
Atkinson, whose father died of cancer, said pro-shooting donors had told him they intended to stop supporting the charity, which spends £45m on cancer research each year, in protest.
"The whole thing is unbelievable," said Atkinson. "They have done severe damage to their credibility."
The institute is refusing to discuss its decision beyond issuing a brief statement.
But Atkinson accused it of hypocrisy for refusing his money while undertaking research projects that bring it into conflict with animal rights groups.
"It's unacceptable for them to use double standards to justify their stance," he said.
Atkinson, who claimed senior institute figures took part in the shoots, said his donation had not yet been returned and that he hoped the charity would change its mind.