The value of the sector's investment assets fell by about 3.1 per cent in 2009, according to figures drawn from the annual reports of charities.
The investment assets of the 1,000 charities with the largest portfolios were valued at about £64.9bn, down from £66.9bn in the previous year, according to data collated from the most recent reports, which mostly had a financial year-end in the month of December 2009.
The income of the top 1,000 charities fell from £13.1bn to £12.5bn, but their charitable expenditure rose from £10.3bn to £10.7bn.
The figures are published in the JM Finn & Co Charity Performance Guide 2010, which measures the investment performance of third sector organisations. The guide will be launched in October.
"Income for these charities is down across most areas," said a spokesman for DG Publishing, the publisher of the guide. "The figures show that this was a difficult time for charities."
Charities saw a fall in equity and property values but a marginal rise in the value of bonds, he said.
DG has published further information about the performance of charity investments at a new website, www.charityperformance.com.