The research showed that the median male chief executive salary had risen by 8 per cent, whereas the equivalent female salary had gone up by only 5 per cent.
The difference in average pay now stands at £11,000, up from just under £8,700 a year ago.
The survey also revealed that women were less likely to hold the top position in large charities.
Although there were more female than male chief executives of organisations with annual incomes of up to £1m, there were more than twice as many male as female chief executives in organisations with incomes of more than £5m.
Stephen Bubb, chief executive of Acevo, said the figures showed that the sector "needed to get its house in order".
He said: "It is shameful that there is a growing gender gap in a sector that champions social justice."