The U.K. bank has drawn criticism this year over its performance and rising bonus pool. In February Barclays announced its investment bank's compensation to income ratio - a measurement of how much of its earnings it pays out in salary and bonuses — had risen to 43.2 percent.
At the time, Barclays chief executive Antony Jenkins said that the bonus increase was as result of the bank's intention to pay competitively to have the right people to drive returns.
Shareholder Philip Clark told the bank's annual general meeting in London's Royal Festival Hall on Thursday that Barclays was still "paying for Manchester United but getting Colchester United."
And when called to vote on the pay proposals, major investor Standard Life rejected them, with Alison Kennedy, the U.K.insurance group's governance and stewardship director, calling for more clarity on the criteria used for bonuses.
However Jenkins told CNBC after the meeting that it was "important to look at the three votes together."
There were three different votes on pay at the meeting: one on the bank's pay to executives last year; another on pay over the next three years and a third to address new European Union laws limiting executive pay.
But Walker pointed out that the majority of shareholders backed the bank's pay proposals, and stressed that deciding on Barclays bankers' pay was a "very difficult" job.
Defending the bank's salary and bonus policy, Walker pointed out that Barclays had to pay to replace the majority of its U.S. Bonds desk last year - and that not being able to trade an investment as important as U.S. Treasurys would have been bad for the bank and its shareholders.
He also suggested that Barclays had reduced its bonus pool too far in the 2011-12 financial year.
At Thursday's annual meeting, the chairman went to great lengths to try to empathize with the bank's smaller investors, pointing out that board members were also shareholders and frequently referring to "your" bank.
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Jenkins emphasized the importance of the bank's strategic review, due May 8 which is expected to involve a trimming of the investment bank.
AGMs usually tend to be sedate affairs, but the years since the financial crisis have seen more obstreperousness from small shareholders.
"The battle is still on the big money front," Harry Braunde, a small shareholder attending the meeting, told CNBC.
"What's important is the ratio of dividends to the pool of money which is held for payment."