Dr Marshall, who has started a number of technology companies in the US, began his career as a cadet at the Defence Science and Technology Organisation.

He will start at CSIRO in January 2015.

An inventor with a PhD in physics, Dr Marshall has lived in the US for 25 years and is currently the managing director of venture capital firm Southern Cross Ventures, based in Silicon Valley.

The firm also has offices in Shanghai, and Dr Marshall has long partnered with major Chinese venture capital firm SoftBank China.

He will replace outgoing chief executive Dr Megan Clark, who has been in the role for the past six years.

Dr Marshall will enter the organisation at a difficult time - funding to the organisation was cut by $111 million over four years in the May federal budget, which will result in more job losses.

The cuts will also force the CSIRO to close eight sites and reduce research in some areas.

The head of the CSIRO's business and commercialisation arm warned the funding cut will have long-term detrimental effects on the nation's ability to innovate.

Former CSIRO scientist Judy Eastham has also raised concerns about the participation of women in the organisation, saying that the proportion of female research scientists decreased in 2012-13 compared with the year before.

"Leaders are instrumental in shaping organisational culture, and commitment from the top is critical to the success of any cultural change initiative," she said in August.

Minister for Industry Ian Macfarlane has welcomed the appointment.

He said Dr Marshall would guide CSIRO through "a significant new phase" in which the institution "will play an increasingly important role in the Australian economy".

Mr Macfarlane said he was pleased with Dr Marshall's commercial experience.

"In particular, his experience in Silicon Valley, research and development and the commercialisation of products and ideas will be valuable in ensuring CSIRO rightfully claims its place at the centre of Australian industry policy," Mr Macfarlane said.

The union representing workers has also welcomed the announcement, but said Dr Marshall would "face significant challenges".

"An immediate challenge for Dr Marshall will be to repair morale and meaningfully involve staff and their representatives in the strategic planning for CSIRO's future," CSIRO staff association secretary Sam Popovski said.

Mr Popovski also paid tribute to Dr Clark. "There should be no doubt regarding the passion and professionalism Dr Clark has brought to the role," he said.