Speaking ahead of the UK Budget to an audience at Edinburgh University, Swinney is expected to call on the Chancellor George Osborne to improve the existing tax framework for research and development (R&D) in the UK to provide the most efficient mechanisms to stimulate investment by innovative industries.
He will point out that Denmark and Finland spend nearly twice as much on R&D as a proportion of GDP as Scotland.
Swinney will say: "Independence - in providing access to all economic levers - would present an opportunity to develop a fully aligned and coherent framework to encourage and support Scottish innovation.
"In [its document] Building Security and Creating Opportunity, the Scottish Government set out financial levers available to support and encourage innovation, including tax incentives such as the WBSO, a payroll tax incentive which currently operates very successfully in the Netherlands.
"Research shows that this type of scheme can have strong positive impacts on SMEs, increasing their R&D spend, helping with cash flow, stimulating demand for innovation and creating high value jobs.''
Swinney will points to Finland as "one of the few high-performance countries with high rates of both higher education R&D and business R&D".
Scottish Culture and External Affairs Minister Fiona Hyslop visited Finland's innovation agency, Tekes, in Helsinki last week.
"The Scottish Government is in active discussion with the Tekes agency,'' Swinney will say.
"If we truly want to see a major change in Scottish business innovation to transform our economy we need full responsibility for innovation support in its entirety, including control of all fiscal levers.
"We could then put this at the command of a high-profile and empowered Scottish Agency for Innovation that would become the engine behind business innovation growth in Scotland."