A spokeswoman for the regulator said the amount owed "could well be more than that". She said the figure was based on initial findings by Pesh Framjee of Crowe Clark Whitehill LLP, who was appointed interim manager of the Dove Trust, the charity that owns the site, on 6 June this year.
The shortfall is the difference between the funds due to the charities donated through the site and the cash held by the Dove Trust.
An estimated 7,000 individual giving pages created by fundraisers have been affected by the site’s suspension, the commission spokeswoman said.
Framjee was due to meet with "a large charity" yesterday in an attempt to ensure charities do not lose out after the suspension of the site. He was unavailable for comment this morning.
The commission spokeswoman said: "We are working to protect charitable funds. While he has been doing his review of the charity’s finances, the interim manager has also been trying to develop a way in which people can still give to those who were fundraising through the site, whether that be with another charity."
The commission suspended the website and announced on Friday that it had appointed Framjee as interim manager. The site was suspended to protect funds donated by the public and prevent further charitable pledges being made through it.
A regulatory compliance case was opened into the Dove Trust in January 2011 because of concerns about its governance and financial management. It has not filed any accounts since the year ending 5 April 2009, when its voluntary income was £3.2m.
The Institute of Fundraising has attempted to reassure donors about giving through online fundraising platforms.
Ceri Edwards, the institute’s director of policy and communications, said: "This should not undermine public confidence in online giving, which is a generally safe way to give, and we would remind people of the many online platforms, some very well known, that enable people to give."
The Charity Commission has said that any donors or charities concerned about the suspension of the site should contact DoveTrustinterimManager@crowew.co.uk or telephone 0207 842 7313.