Figures published by the Daily Mail show they typically earn £32,711 a year, compared to the £43,316 median average recorded for men.
They emerge two months after the Archbishop of Canterbury condemned the UK-wide gender pay gap of 8.6 per cent as unfair.
The statistics include almost 500 members of staff working at bodies including the Church of England's financial wing, the Church Commissioners; and its executive body, the Archbishop's Council.
They do not include clergy and other workers employed locally by individual dioceses.
A spokesman told the Mail that the gender pay gap had shrunk since last year but there are still fewer women holding senior posts.
They said: "We continue to see a large proportion of females in the lower and mid-lower quartiles compared to the UK average; this subsequently impacts on the average pay for females being lower than males."
Carole Harden from the National Church Institutions - the collective name for seven national Church of England bodies - told the newspaper: "This year's results are encouraging as we continue to review pay structures, addressing any imbalances and barriers to females and opportunities for advancement within the NCIs.
"We are committed to improving this further as we focus on reducing the difference in pay between men and women in more highly paid roles, and improving the ratio of men to women in the most senior and most junior roles."
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