Only two of the Jewish charities surveyed, Norwood and South London care home Nightingale House, reached the average score of 68 per cent.
The 10 charities with the lowest scores out of the 500 surveyed by IG this year were all Jewish.
Last year, a survey by the agency found similar results.
Adam Rothwell, director of IG, said: "Many of the Jewish charities have stayed at the bottom again this year, making them among the least transparent in the country. It is very disappointing.
"There are 10 Jewish charities scoring under 40 per cent, meaning they would make up the bottom 10 of all the 500 charities we have profiled this year."
Some of those scoring the worst included JNF, the Jewish Leaning Exchange, and the Oxford Centre for Jewish and Hebrew Studies.
The worst performer was Cosmon (Belz), which works to advance Orthodox Judaism. It scored just 20 per cent, a 30 per cent drop from last year.
Mr Rothwell explained: "It doesn't really take much effort to get over 60 per cent, so these charities are not taking transparency and openness very seriously.
"There's such a dearth of information about them and they are so reticent that it makes it look like they are trying to hide something."
But it was not all doom and gloom.
Care home Nightingale House scored 75 per cent, making it one of IG's top-ranked charities. And UJIA and the Manchester Jewish Federation, both of which scored badly last year, made huge improvements this year.
UJIA, which achieved only 32 per cent last year, has now scored 59 per cent, while the Fed went up from 29 per cent last year to 63 per cent this year.
"Their improvements are totally unprecedented," Mr Rothwell said.
"The Manchester Fed has totally transformed its attitude to making information available to the public and to informing people about its work. UJIA has also done fantastically and has totally changed its culture of reporting."
Intelligent Giving was set up five years ago to provide a web-based guide to donors on how different charities spend their money.
www.intelligentgiving.com/
