Andrew Hind, chief executive at the commission, said last week that his body's expected new duty to explain the sector to the general public, as outlined in the Charities Bill, could have a perverse outcome because knowledge of charities was so low.
The Bill, being debated in the House of Lords today, gives the commission a new public affairs role with the objective of increasing public trust and confidence in charities.
"If we're not careful, we could do a lot of good work and yet appear, at a superficial level, to drive down confidence in the sector," Hind told members of the Charity Investors' Group.
Lindsay Driscoll, legal commissioner at the Charity Commission, said public confidence in charities was very high but added that ignorance was rife. Most people thought the Body Shop was a charity, she added, but few knew that Eton had charitable status.
The regulator last week appointed consultancy AS Biss to help with its new public affairs function.
As the Bill returns to the Lords today for its report stage, peers are being urged to back an amendment intended to defuse the controversy over the charitable status of public schools and fee-paying private hospitals.
Tabled by LibDem peer Lord Phillips of Sudbury, the amendment would require the Charity Commission to "consider the effect on public benefit of the charging policy of any charity" when carrying out consultation before issuing guidance on public benefit.
The Bill removes a long-standing presumption of public benefit by organisations providing education, religion and relief of poverty, and makes the commission the arbiter of whether charities are meeting public benefit criteria to justify their charitable status.
The amendment is being backed by the NCVO and other members of the Coalition for a Charities Act.