The country's largest 5,000 charities listed a combined pensions deficit of £1.66bn in their most recent accounts, according to research from charity data website Charity Financials.
The site found that 522 of the top 5,000 charities operated a defined-benefit pension and these groups had seen their pension deficits rise by more than 50 per cent over the past two years.
A spokesman for Charity Financials said: "As in most economic cycles, the markets will bounce back – and when they do, there will be an increase in the value of pension scheme assets.
"This will go some way towards reducing the overall long-term liability in years to come. In the meantime, charities and social enterprises have a major challenge in managing the impact of this potentially huge problem."