Asked to rate their trust in charities on a scale of 0 to 10, members of the public recorded a mean score of 6.3 in the survey, which was conducted in February.
Confidence in charities was also "grounded in faith rather than any rationally based expectation", pollster Opinion Leader Research concluded.
The research was carried out by the commission in preparation for a new statutory objective "to increase public trust and confidence in charities", which forms part of the Charities Bill.
Opinion Leader Research described the score of 6.3 as moderate: "Although not poor, it certainly does not allow for complacency, and trust and confidence will require careful monitoring."
Faith in the sector is based on shaky foundations, the survey found.
Most people had an "inherent belief" that charities will spend donations wisely, rather than real knowledge of how charities work. Although 79 per cent of the public felt most charities were inherently trustworthy, 69 per cent admitted they did not know much about how they are run.
"It's good news that so many people inherently believe that charities are well-managed," said Andrew Hind, chief executive of the commission.
"But this basic level of trust seems to be based on a more limited understanding of the issues than we had expected. This adds up to another challenge to charities, and the commission, to better explain the role of the sector."
Trust in the sector proved highest among those who work for a charity, and those aged between 35 and 44. It was lowest among black and minority ethnic groups, which posted a trust 'score' of 5.4 per cent.
The survey found that many members of the public were mistaken about which organisations hold charitable status. Nearly two-thirds of respondents believed Amnesty International was a charity, whereas only 7 per cent knew that Eton was.
- Trust in charities is moderate. Sector scores 6.3 out of 10 in public trust survey
- Most people feel that charities are trustworthy but don't know how they work
- Trust is highest among those aged 35-44 and lowest among ethnic minorities
- There is poor public knowledge of charitable status. Only 7 per cent know Eton has charitable status.