The takeover target also raised concerns that the deal may entail problems over effective integration of the two banks.
A statement from Bendigo said: "The proposal involves significant risks, including integrating organisations with different business models and philosophies. The Bendigo Bank Board has concluded that the Bank of Queensland proposal is not in shareholders' best interests."
BoQ had identified the bank as a target which would better enable smaller regional banks to compete against the four banking giants such as Macquarie which dominate the market to the extent that they control all but 20 per cent of banking assets.
Meanwhile, David Liddy, managing director BoQ, expressed disappointment at the bid's rejection.
He told news.com: "We strongly believe in the compelling logic for the merger and the shareholder value which would be created. Together we are natural allies against the big banks."
Should the deal have gone through it would have created the seventh-largest bank in Australia.
Since news of the rejected offer broke, Bendigo's shares dipped by 6.6 per cent, while BoQ shares dropped by 2.4 per cent.