Only 86 charities have entered this year's awards, compared with 553 in 2002, when the competition was for print-based entries.
Last year, competition sponsors CAF and the Institute of Chartered Accountants of England and Wales decided to limit the contest to internet entries in a bid to improve the sector's online annual reports.
But this has deterred large swathes of charities, with numbers down across all categories. Only 20 entered the section for more than £2m income, 17 the £500,000-£2m section, 16 the £100,000-£500,000 section and 20 the less than £100,000 section.
These entries are being judged currently, and the winners will be announced at CAF's annual conference in November.
Concern has been expressed that smaller charities, which enter the competition to get feedback on the quality of their annual reports, could lose out on a valuable source of advice.
One charity, which felt discouraged from entering, was Harvest Help, the runner-up in last year's competition in the £500,000-£2m category.
Fundraiser Sharon Jackson said: "They were looking for something far more interactive than we are able to do. We have a free service provider and this limits what we can do with the site. It's good that they've highlighted online accounts, but we have neither the time nor the internet hosting to be in the ball park."
A CAF spokeswoman said that the low entry numbers had been anticipated.
"We knew it would be a learning curve for all concerned, but this is no different to the launch of the original competition, when we received a handful of entries," she said.
But competition judge and deputy chief executive of WWF-UK, Les Jones, called for next year's competition to introduce a transition period, allowing for print-based entries. "The number of entries is very much down. There should be an element for conventional accounts," he said.