Home Office officials are holding talks with GuideStar about the future of the new charity information website, which goes live to the public on 12 December but will run out of funding in four months.
GuideStar hopes to continue in its present form with a combination of renewed government funding and income from selling licences for more advanced uses of its database of 167,000 charities.
The Charity Commission has also had discussions with GuideStar about integrating it with its own register of charities if it fails to stay independent.
GuideStar received £2.7m from the Treasury's Invest To Save programme and obtained grants from foundations to meet the startup total of £4.6m.
With its test site now running, it is stepping up its marketing of licences.
Erica Roberts, chief executive of Guidestar, said it had sold a licence to the NCVO to use GuideStar data for its annual almanac and had "six or seven other possible contracts at various stages of negotiation".
Andrew Hind, chief executive of the Charity Commission, said the organisation could take on GuideStar only "on a restricted basis" unless it received extra funding to run the site.
He said the commission would want to restrict the level of detail on smaller charities and use different criteria for information posted by charities themselves. "We understand the content is not being mediated," he said.
Meanwhile, two academics have renewed their criticism. Adrian Sargeant of Bristol Business School and Stephen Lee of Henley Management College said their survey of the test site suggested it was not worth the wait or the expense.
They said it was too similar to the Charity Commission website, there was insufficient transparency about startup funders and the data the site contained offered "no basis for assessing the performance of a charity".
Roberts countered that GuideStar's technology was far in advance of the commission website, especially the local search facility, which was being widely used on the test site. Trust and foundation startup funders preferred to disclose their contributions on their own websites, she said.
"We like to see ourselves as the Yellow Pages for charities," Roberts said. "More than 10,000 charities have added information to their entries, nearly all of them small organisations. There is a demand for it and, when people search, it's usually to find out what's in their neighbourhood."