Twenty-eight per cent of charity chief executives have had their salaries frozen in the past year, according to Acevo's annual pay survey.
The survey of members of the chief executives body, published today, also reveals that leaders of small charities with annual incomes below £150,000 have seen their salaries fall by 9.1 per cent to a median average of £33,600.
By contrast, chief executives of charities in the £25m-£100m income bracket saw a 1.7 per cent increase in wages to a median of £104,500.
Overall, median pay for chief executives fell from £57,300 to £57,264.
Stephen Bubb, chief executive of Acevo, said charity leaders had shown "commendable" pay restraint during the recession compared with their private sector counterparts.
A survey in The Guardian last month showed directors' salaries at large private companies had increased by an average of 10 per cent.
"Charity chief executives are shouldering much of the financial burden of the recession," said Bubb.
"In the private sector, salaries continue to go up regardless, and banking salaries are disgustingly irresponsible. But charity chief executives take their responsibilities seriously."
He added: "We must not allow the current situation to become the norm. It is important that we continue to make the case for paying charity chief executives fairly."
Forty-two per cent of the 707 chief executives polled said they had suffered either increased workload or stress. Bubb said this was worrying, and said calls to Acevo's CEO in Crisis helpline had tripled over the past year.
Researchers, who also quizzed 206 chairs, found that 93.5 per cent of chief executives and 91.7 per cent of chairs were white. Men were almost twice as likely as women to be chairs.
Tesse Akpeki, a governance consultant, said the recession might have prompted some organisations to lose their focus on diversity.
She added that many non-white people wanted to serve on boards, and charities needed to rely less on word of mouth and more on new methods, such as social networking websites Twitter and Facebook, to recruit them.
The survey found the median salary for female chief executives had risen while male salaries had fallen, reducing the gender pay gap from £11,000 to £7,550.