Fiona Hyslop, in a new letter to Creative Scotland's chairman Sir Sandy Crombie, has called for the body to find the "correct balance" between funding artists and commissioning new work.
She says transparency in its dealings is needed to build trust. Earlier this year, Ms Hyslop told The Herald she regarded Creative Scotland as primarily "not a commissioning body" but acknowledged it does have a role in the co-ordination and commissioning of large cultural programmes, such as the Cultural Olympiad and the 2014 Commonwealth Games.
Creative Scotland, however, has set aside more than £3 mil-lion for a new scheme, called "strategic commissioning", which is funded by its core grant from the Government and not National Lottery money. Some have questioned the scheme, as it could be interpreted as giving the funding body an "artistic director" role.
In her letter, Ms Hyslop asks for clarity in the body's dealings with artists and its controversial commissioning role.
She writes: "I am also keen to provide clarity on the matter of Creative Scotland's role with regard to commissioning. Creative Scotland's primary role is to invest in artists and talent and quality production of the arts and film in a way that increases public engagement with arts and culture and helps both artists and all forms of creativity thrive in Scotland.
"The majority of your budget is spent on cultural organisations and in funding applications from artists, film-makers and others who want to realise their creative ideas for the benefit of Scotland."
She says she supports Creative Scotland's plans to strategically commission programmes of work "that help fill gaps in cultural provision, build on existing strengths or meet a specific objective, for example to support the [recent] Theatre Review recommendations".
However, she adds: "I know you will consider carefully the correct balance between the range of commissioned and open access funding for artists and cultural organisations.
"It may be that the use of the term 'commissioning' is causing confusion, since it has such a broad definition – this is something you may wish to clarify in your updated corporate plan."
Andrew Dixon, chief executive of Creative Scotland, said he believed the balance had been struck, with 80% of its funds used to support artists and 20% spent on commissioned work.
The new letter was written to Mr Crombie following further feedback from the arts sector.
Criticism of the body has continued recently, with leading publisher Hugh Andrew of Birlinn criticising its "leaden apparatchik-speak" and "millions of pounds being squandered on meaningless projects by bureaucrats safely esconced on salaries far higher than most in the arts world".