Five hundred of the 167,000 charities contacted by GuideStar attempted to log on after the site went live on 7 September.
Each charity had been posted a unique password to access the site and then had to choose another password to log on.
"The two stages of registration and log-in were confusing," said Audrey Poppy, communications manager at GuideStar.
She apologised for the problem and said the number of charities that visited the site confirmed the sector's enthusiasm for the project, which is intended to improve transparency by putting charity data online.
The site is due to open to the public later this year.