The writer, whose work inspired Hollywood films Kick Ass and Wanted, said its policies were "entirely sensible for a body designed to build jobs and solid arts infrastructure".
Mr Millar, whose Kick Ass 2 film starring Jim Carrey and Nicolas Cage is being shot in England and Canada, said that if the body is "thinking mainstream" then the "policy is a good one".
His comments come after a stinging broadside from Don Paterson, the leading Scottish poet, who described the body as a "dysfunctional ant-heap".
Creative Scotland has been under fire in the arts community since it announced the scrapping of its regular Flexible Funding for more than 40 companies, plus unpopular decisions such as funding a cookery show to be made by STV.
The award-winning poet, honoured with the Queen's Gold Medal for Poetry in 2010, also criticised the idea of the Year of Creative Scotland in an article entitled A Post-Creative Scotland, which will appear in a book entitled Unstated: Writers on Scottish Independence, to be published by WordPower books in November.
Mr Paterson said Creative Scotland should be abolished and said it was the product of "a shocking SNP policy vacuum and a New Labour neo-managerialism incapable of understanding the difference between art and business".
The poet and editor said the £6.5 million Year of Creative Scotland was guilty of "vapidity and cynicism".
However, Mr Millar defended the chief executive of Creative Scotland, Andrew Dixon, saying his "policy is a good one".
"He's trying to help people asking him for finance to reach the widest possible audience," he said. "If you're a guy running a show like that with a limited amount of cash and an infinite amount of artists and writers needing it for a pet project you're always going to make enemies.
"It's hard because everybody thinks their project deserves to be funded or, if not theirs, a project their friend has been working on.
"But [Mr Dixon] has done a really good job and is moving in the right direction by asking creative people to be a little more savvy. Personally, I'm uncomfortable with the state being involved in culture at all – it's our job, as writers and artists, to be suspicious of government. All we need is a pen and paper."
Next week, Mr Dixon will appear at the Culture Committee of the Scottish Parliament, which will question him on the past year's activity at the funding body.
MSPs will hear that the vital infrastructure of the arts is facing "wanton destruction", papers released yesterday said.
In a written submission, public artist Matt Baker, who will also appear before MSPs, drew attention to the funding model. "The strategy seems to be to remove the core funding and instead support individual projects on the premise that this targeted support will allow/encourage organisations to become self-sustaining and independent of ongoing support," he writes.
"This strategy applied from a centralised national body, and without a complementary package of other measures, cannot work and will cause wanton destruction of vital arts infrastructure in the country."
A Scottish Government spokeswoman said: "The celebration of the year has embraced more than 5000 events and activities all over the country. All of these have benefited from extensive marketing and PR activity by VisitScotland."
Contextual targeting label: