Figures from PayFinder, which compares the salaries of 140,000 employees in 50 industries, show that voluntary organisations rank 37th.
The average sector wage of £22,879 puts charity workers ahead of counterparts in agriculture, restaurants and catering and tourism, but behind PR, construction and education. The best paying sector is energy and natural resources.
The statistics also show a gender gap, with men in the not-for-profit sector earning an average of £25,747 and women £22,313.
"The short-term nature of funding is one of the main reasons behind low pay," said Mike Short, national officer for the community and voluntary sector at the trade union Unison, which represents 50,000 charity staff.
"It makes it far more difficult for service providers to plan for decent wages and incremental pay rises."
He said Home Office support for longer-term funding suggested that "things were moving in the right direction" but that morale would suffer and the quality of services would fall unless more action was taken.
The survey does little to dispel the myth that charities are regarded as a cheap option for delivering services. Local government employees can expect to be paid £27,081 a year on average, which is £4,000 more than charity staff take home.
Richard Evans, chief executive of voluntary sector headhunter CF Appointments, agreed low pay was an issue for the sector but said it was dangerous to paint a homogeneous picture.
"There is some evidence at middle and senior management level that some salaries are beginning to improve," he said.
A charity's size was another crucial variable, he added: "Larger charities can afford to pay more, and some are beginning to compare favourably with the public and private sectors. At the other end, a huge number of low salaries tend to be paid by smaller charities."
Payfinder's figures for the voluntary sector, which are based on more than 4,000 anonymous entries to the organisation's website, suggest that a chief executive is not always the best paid employee in a charity.
They earn an average of £44,450, which puts them behind finance directors, operations directors and marketing directors, who top the poll with an average salary of £47,583.
A communications manager can expect to pocket £28,333, and a fundraising manager has to settle for £26,792.