Intelligentgiving.com accused CIN of using "clever wording" to mislead donors into believing the charity has no administration costs, and criticised the reporting methods of several other well-known charities.
The institute, which has also criticised charities claiming to have no administration costs, called the site's methods crude and rudimentary. "The recent news stories highlight the need for a sensible debate in the press about openness and transparency in charities," said Lindsay Boswell, the institute's chief executive.
"Coverage like this potentially threatens the ability of charities to fundraise and be a force for good."
David Pitchford, the site's founder, defended its methods. "We couldn't agree more that there's a need for a 'sensible and balanced debate'," he said. "We don't see anyone besides Intelligent Giving bringing that debate to the table.
"We have a policy of refining our criteria, and we already have new prospective criteria planned, based on the work of Keystone Reporting, an internationally respected accountability organisation," he said.
Children in Need broke its previous fundraising record, taking £18.3m last Friday; it raised £17m last year.