Giving evidence to the Scottish Parliament Communities Committee last week, Jane Ryder said she supported the principles of the Charities and Trustees Investment Bill (Scotland), including the definition of public benefit.
She said the Bill "will enable us to develop a framework that will allow charities to flourish for years to come and retain public confidence in the sector".
The Bill includes a charity test that states organisations must be exclusively charit-able, as well as a public benefit test.
National Museums of Scotland, the Scottish Arts Council and Sport Scotland are among the public bodies that could lose their right to be called a charity.
Their status as non-departmental public bodies, subject to directions from the Scottish Executive, means that they will not pass a new robust test of independence in the Bill (Third Sector, 12 January).
The legislation would carry a similar threat to fee-paying schools.
Ryder added: "Parliament needs to strike the right balance between principled consistency and a pragmatic response to dealing with both legacy and future expectations."
Her stance is backed by the Scottish Council for Voluntary Organisations.
"We need to be clear about what a charity is," said a spokesman for the umbrella body. "Charities need to be independent of government controls and we want the existing confusion removed."