Research by the chief executives body showed that the median pay for heads of charities with annual incomes of less than £150,000 had risen to £37,000 - an increase of £7,000.
The Acevo Pay Survey 2008/09 asked almost 700 charity chief executives about their salaries. It showed that pay for heads of charities of all sizes rose by an average of 8 per cent to a median of £57,300.
The median salary for chief executives of charities with annual incomes of between £150,000 and £250,000 rose by almost 10 per cent.
Ralph Michell, policy advocate at Acevo, said the 23 per cent rise was a positive development. The role that chief executives played in getting results should be rewarded, he said.
"In order to get the right outcomes, you need to have chief executives in place who know what they are doing, and you need to pay for that," he said. "We should not be ashamed of it."
Although the survey covered only 26 chief executives from charities with incomes of less than £150,000 a year, the figure should be seen as indicative for the rest of the sector, said Michell.
Neil Cleeveley, director of policy and communications at local umbrella body Navca, said his organisation's members were not reporting a comparable rate of pay rises.
"We are currently seeing local third sector groups coming under the twin pressures of rising costs and rising demand for the services they provide," he said.
"In these circumstances, we are surprised at this reported increase in chief executive salaries."
The survey also showed that fewer than one in three charity boards had any trustees from ethnic minority groups.