The NCVO is holding discussions with a database supplier about teething problems on its Government-funded grants directory website, Funding Central.
A spokesman for the umbrella body said some users had complained to it about being unable to access the site's content. He said the NCVO was in discussions with j4b, the organisation providing the funding database, about the problem.
Jeremy Phillips, managing director of j4b, said a team of four was working to resolve the problems.
The Office of the Third Sector is paying the NCVO £1.6m over the course of three years to run the site, which was launched earlier this month. It lists opportunities for funding through grants and contracts and is free to use.
Some charity workers have said the website is misleading and content is hard to access. Paul Brown, social enterprise business adviser at urban regeneration charity the Eldonian Group, contacted Third Sector and said he had been unable to access any helpful information and that the site would not produce a list of funds to which he could apply.
"It's very frustrating," he said. "At the moment I pay to use the Directory for Social Change's government funding site, so I was keen to look at this site because it was free. If it worked properly, I wouldn't renew my DSC subscription. Although Funding Central costs nothing, you get nothing in return either."
Another charity worker, who contacted Third Sector but asked not to be named, said the site's claim to list more than 4,000 funding opportunities was misleading. "Funding Central uses its high number of entries as a selling point, but 150 of the entries are Grassroots Grants, which should count only as one funding opportunity," he said.
There were many contracting opportunities on the site that were totally irrelevant to the sector, he said, and should have been removed. "I found offers of contracts for the provision of insurance services and the supply of syringe pumps," he said. "I can't think of any charity that would bid for these."
An NCVO spokesman said: "A number of contracting opportunities might not on the surface appear to be relevant. But in line with the procurement guidelines, these opportunities are open to bids from the third sector."
The NCVO will be holding focus groups this summer to ask users about their experiences of the site, he added.