The research, conducted by pay and benefits consultancy Croner Reward, was based on 8,097 job records provided by 348 charities.
The findings show that pay for chief executives in charities averaged £65,000 in 2006, 20 per cent below the all-sector median of £81,160. This pay gap has fallen from 22.6 per cent in 2005, but has not closed sufficiently to reach the 2000 level of 17.3 per cent.
The situation in the capital is even worse, with London-based charities paying 25 per cent below the overall median at director and senior executive level.
Pay for heads of functions in the sector is 18 per cent lower than the overall median. This figure rises to 26 per cent in London. For middle managers the differences are 10 per cent and 13 per cent respectively.
Vivienne Copeland, client services director at Croner Reward, said: "Charities are still inclined to rely quite heavily on the desire to 'make a difference' to compensate for lower than average pay.
"However, the growing level of professionalism and commercial realisation means that charities are more willing to pay 'commercial' rates for hard-to-recruit and important roles."
Lai-Har Cheung, employment practice manager for the Workforce Hub, said the figures did not paint a full picture and that the gap could be explained partly by the fact that voluntary sector employees were more likely to fill part-time jobs or be on temporary contracts.
Cheung said: "While the sector may be behind on pay, it is better at offering its employees benefits such as family-friendly policies. It would be naive to expect pay comparable to working for BP: you are not comparing like with like."
But Copeland said there were significant parallels between the private and voluntary sectors. "The demands and pressure on those at a senior level in the sector are significant and comparable to the situation in big companies," she said.
Directors and senior managers in engineering, science and research are the best paid executives of all.
Welfare services directors are the second highest paid.
Below the managerial level, finance, computing and legal jobs are the highest paid.
Fundraisers appear mid-table in the pay league, along with administrators.